NPASS Compound

Structure

CID3852 OpenBabel06191715322D 39 40 0 0 1 0 0 0 0 0999 V2000 2.3184 0.7394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3184 2.4715 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3012 5.3480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3719 4.8997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0377 -1.5432 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6844 1.1055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3366 2.4502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1215 -0.2387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4316 -1.0555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3184 2.4715 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8188 3.4161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8184 1.6055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1471 3.6749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5337 -1.0477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9459 -1.8567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7252 -0.1741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5629 0.4188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3184 2.4715 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0776 2.4502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9820 -0.8432 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5106 -0.5799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8184 1.6055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4060 4.6408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6309 -2.4567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5282 -1.1523 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.3184 0.7394 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6293 0.7771 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9514 -1.7522 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.8184 1.6055 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3705 1.7431 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1160 -0.3432 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5446 -0.8387 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2187 -3.2657 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9349 -2.0658 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6844 2.1055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5954 1.4843 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3636 -2.5612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3239 0.6349 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 22 1 0 0 0 0 2 22 1 0 0 0 0 3 23 1 0 0 0 0 4 23 1 0 0 0 0 5 24 1 0 0 0 0 10 12 1 0 0 0 0 10 18 1 0 0 0 0 11 13 1 0 0 0 0 11 19 1 0 0 0 0 12 22 2 0 0 0 0 13 23 2 0 0 0 0 14 15 1 0 0 0 0 14 25 1 0 0 0 0 16 20 1 0 0 0 0 16 26 1 0 0 0 0 17 21 1 0 0 0 0 17 27 1 0 0 0 0 18 29 1 0 0 0 0 19 30 1 0 0 0 0 20 31 1 0 0 0 0 21 32 1 0 0 0 0 24 33 2 0 0 0 0 24 37 1 0 0 0 0 25 31 1 0 0 0 0 25 34 1 6 0 0 0 26 29 1 1 0 0 0 26 38 1 0 0 0 0 27 30 1 1 0 0 0 27 39 1 0 0 0 0 28 15 1 6 0 0 0 28 32 1 0 0 0 0 28 37 1 0 0 0 0 29 6 1 1 0 0 0 29 35 1 0 0 0 0 30 7 1 6 0 0 0 30 36 1 0 0 0 0 31 8 1 6 0 0 0 31 38 1 0 0 0 0 32 9 1 1 0 0 0 32 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	552.4
Volume:	598.537
LogP:	6.184
LogD:	3.849
LogS:	-4.605
# Rotatable Bonds:	15
TPSA:	105.45
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.181
Synthetic Accessibility Score:	5.366
Fsp3:	0.844
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.746
MDCK Permeability:	1.647538192628417e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.827
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.17
30% Bioavailability (F30%):	0.444

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.031
Plasma Protein Binding (PPB):	84.89762115478516%
Volume Distribution (VD):	1.38
Pgp-substrate:	6.853207111358643%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.072
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.82
CYP2C9-inhibitor:	0.025
CYP2C9-substrate:	0.034
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.038
CYP3A4-inhibitor:	0.42
CYP3A4-substrate:	0.306

ADMET: Excretion

Clearance (CL):	7.909
Half-life (T1/2):	0.104

ADMET: Toxicity

hERG Blockers:	0.177
Human Hepatotoxicity (H-HT):	0.967
Drug-inuced Liver Injury (DILI):	0.096
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.026
Skin Sensitization:	0.931
Carcinogencity:	0.081
Eye Corrosion:	0.004
Eye Irritation:	0.03
Respiratory Toxicity:	0.033

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC3852

Natural Product ID:	NPC3852
*Common Name:**	[(1S,4R)-4-Hydroxy-1-[(2R,5R)-5-[(2S)-2-Hydroxy-6-Methylhept-5-En-2-Yl]-2-Methyloxolan-2-Yl]-4-[(2S,5R)-5-[(2S)-2-Hydroxy-6-Methylhept-5-En-2-Yl]-2-Methyloxolan-2-Yl]Butyl] Acetate
IUPAC Name:	[(1S,4R)-4-hydroxy-1-[(2R,5R)-5-[(2S)-2-hydroxy-6-methylhept-5-en-2-yl]-2-methyloxolan-2-yl]-4-[(2S,5R)-5-[(2S)-2-hydroxy-6-methylhept-5-en-2-yl]-2-methyloxolan-2-yl]butyl] acetate
Synonyms:
Standard InCHIKey:	OWELNYSCYCAGMZ-SXSDURSUSA-N
Standard InCHI:	InChI=1S/C32H56O7/c1-22(2)12-10-18-29(6,35)26-16-20-31(8,38-26)25(34)14-15-28(37-24(5)33)32(9)21-17-27(39-32)30(7,36)19-11-13-23(3)4/h12-13,25-28,34-36H,10-11,14-21H2,1-9H3/t25-,26-,27-,28+,29+,30+,31+,32-/m1/s1
SMILES:	CC(=CCC[C@@]([C@H]1CC[C@@](O1)(C)[C@@H](CC[C@@H]([C@@]1(C)CC[C@@H](O1)[C@](CCC=C(C)C)(O)C)OC(=O)C)O)(O)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL303104
PubChem CID:	11786187
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	leaves	n.a.	n.a.	PMID[12828478]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	Roots	n.a.	n.a.	PMID[14575431]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	n.a.	root	n.a.	PMID[15520511]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	seeds	n.a.	n.a.	PMID[15620254]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	seeds	n.a.	n.a.	PMID[1624939]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17027268]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	root	n.a.	PMID[1800638]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	roots	n.a.	n.a.	PMID[19299148]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO11530	Heterosigma akashiwo	Species	Chattonellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19659728]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[19715321]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19919052]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[19931461]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23403897]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24467387]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	roots	n.a.	n.a.	PMID[25066952]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25905468]
NPO5401	Monanchora unguiculata	Species	Crambeidae	Eukaryota	n.a.	n.a.	n.a.	PMID[28368118]
NPO9644	Euphorbia resinifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29667820]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9644	Euphorbia resinifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9644	Euphorbia resinifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO893	Helichrysum sutherlandii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2084	Acinetobacter calcoaceticus	Species	Moraxellaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12988	Blainvillea latifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13692	Leontice kiangnanensis	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6626	Pteris spinulosa	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20318	Acinetobacter baumannii	Species	Moraxellaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5401	Monanchora unguiculata	Species	Crambeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12026	Papaver radicatum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11072	Geigeria schinzii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2505	Pachycereus pringlei	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20383	Stenocereus thurberi	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9375	Medium grandiflorum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO6014	Goniothalamus undulatus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14280	Helichrysum angustifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO893	Helichrysum sutherlandii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3576	Bersama swinnyi	Species	Melianthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13494	Prosopis kuntzei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13798	Cheilanthes marantae	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3924	Penicillium alutaceum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22888	Lophiostoma vaginatispora	Species	Lophiostomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11530	Heterosigma akashiwo	Species	Chattonellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12890	Ophryosporus charua	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9024	Aralidium pinnatifidum	Species	Torricelliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8640	Nemuaron humboldtii	Species	Atherospermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9644	Euphorbia resinifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13604	Dermocybe cardinalis	Species	Cortinariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8820	Lophocereus marginatus	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1418	Boletinus paluster	Species	Gyrodontaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12577	Pinus glauca	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8220	Russula sardonia	Species	Russulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT27	Others	Unspecified		IC50	=	0.52	ug.mL-1	PMID[483393]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC3852 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	173
0.1-0.2	1364
0.2-0.3	6160
0.3-0.4	15983
0.4-0.5	8167
0.5-0.6	8113
0.6-0.7	2426
0.7-0.8	300
0.8-0.85	9
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8889	High Similarity	NPC16964
0.8649	High Similarity	NPC306085
0.8356	Intermediate Similarity	NPC193029
0.8356	Intermediate Similarity	NPC473357
0.814	Intermediate Similarity	NPC158388
0.814	Intermediate Similarity	NPC478003
0.814	Intermediate Similarity	NPC478004
0.8125	Intermediate Similarity	NPC476701
0.8118	Intermediate Similarity	NPC309656
0.8052	Intermediate Similarity	NPC476709
0.8046	Intermediate Similarity	NPC12172
0.8046	Intermediate Similarity	NPC208886
0.7976	Intermediate Similarity	NPC475206
0.7955	Intermediate Similarity	NPC81419
0.7955	Intermediate Similarity	NPC179746
0.7952	Intermediate Similarity	NPC231601
0.7927	Intermediate Similarity	NPC118116
0.7875	Intermediate Similarity	NPC40049
0.7875	Intermediate Similarity	NPC476703
0.7841	Intermediate Similarity	NPC184463
0.7841	Intermediate Similarity	NPC208839
0.7841	Intermediate Similarity	NPC30515
0.7816	Intermediate Similarity	NPC473564
0.7816	Intermediate Similarity	NPC307411
0.7816	Intermediate Similarity	NPC133450
0.7805	Intermediate Similarity	NPC472948
0.7778	Intermediate Similarity	NPC181838
0.7778	Intermediate Similarity	NPC137345
0.7738	Intermediate Similarity	NPC239308
0.7727	Intermediate Similarity	NPC474761
0.7727	Intermediate Similarity	NPC177668
0.7727	Intermediate Similarity	NPC476004
0.7727	Intermediate Similarity	NPC51004
0.7711	Intermediate Similarity	NPC77003
0.7711	Intermediate Similarity	NPC474894
0.7701	Intermediate Similarity	NPC58219
0.7701	Intermediate Similarity	NPC202672
0.7701	Intermediate Similarity	NPC476708
0.7701	Intermediate Similarity	NPC177629
0.7683	Intermediate Similarity	NPC86971
0.7674	Intermediate Similarity	NPC241360
0.7674	Intermediate Similarity	NPC293136
0.7674	Intermediate Similarity	NPC311163
0.7674	Intermediate Similarity	NPC132940
0.7662	Intermediate Similarity	NPC472947
0.7654	Intermediate Similarity	NPC84360
0.7647	Intermediate Similarity	NPC3464
0.7647	Intermediate Similarity	NPC475963
0.7647	Intermediate Similarity	NPC156804
0.7647	Intermediate Similarity	NPC151176
0.764	Intermediate Similarity	NPC472468
0.7625	Intermediate Similarity	NPC93213
0.7619	Intermediate Similarity	NPC103171
0.7614	Intermediate Similarity	NPC92974
0.76	Intermediate Similarity	NPC250836
0.7595	Intermediate Similarity	NPC477085
0.759	Intermediate Similarity	NPC103634
0.7586	Intermediate Similarity	NPC248602
0.7586	Intermediate Similarity	NPC258068
0.7586	Intermediate Similarity	NPC476583
0.7586	Intermediate Similarity	NPC186148
0.7586	Intermediate Similarity	NPC179659
0.7586	Intermediate Similarity	NPC20533
0.7582	Intermediate Similarity	NPC36954
0.7558	Intermediate Similarity	NPC475268
0.7558	Intermediate Similarity	NPC329838
0.7558	Intermediate Similarity	NPC292809
0.7558	Intermediate Similarity	NPC39279
0.7558	Intermediate Similarity	NPC235809
0.7558	Intermediate Similarity	NPC9678
0.7558	Intermediate Similarity	NPC473156
0.7558	Intermediate Similarity	NPC120398
0.7558	Intermediate Similarity	NPC471494
0.7558	Intermediate Similarity	NPC39167
0.7558	Intermediate Similarity	NPC196911
0.7558	Intermediate Similarity	NPC77871
0.7558	Intermediate Similarity	NPC471379
0.7558	Intermediate Similarity	NPC322529
0.7558	Intermediate Similarity	NPC329615
0.7558	Intermediate Similarity	NPC202055
0.7558	Intermediate Similarity	NPC319036
0.7558	Intermediate Similarity	NPC25764
0.7558	Intermediate Similarity	NPC470400
0.7558	Intermediate Similarity	NPC471567
0.7558	Intermediate Similarity	NPC473671
0.7556	Intermediate Similarity	NPC212486
0.7556	Intermediate Similarity	NPC476300
0.7556	Intermediate Similarity	NPC475912
0.7531	Intermediate Similarity	NPC469880
0.7529	Intermediate Similarity	NPC5958
0.7529	Intermediate Similarity	NPC11620
0.7528	Intermediate Similarity	NPC472466
0.7527	Intermediate Similarity	NPC187268
0.75	Intermediate Similarity	NPC234077
0.75	Intermediate Similarity	NPC39754
0.75	Intermediate Similarity	NPC242364
0.75	Intermediate Similarity	NPC191929
0.75	Intermediate Similarity	NPC287164
0.75	Intermediate Similarity	NPC81045
0.75	Intermediate Similarity	NPC151403
0.75	Intermediate Similarity	NPC61257
0.75	Intermediate Similarity	NPC274446
0.75	Intermediate Similarity	NPC171135
0.75	Intermediate Similarity	NPC100454
0.75	Intermediate Similarity	NPC320569
0.75	Intermediate Similarity	NPC133730
0.75	Intermediate Similarity	NPC160540
0.75	Intermediate Similarity	NPC172821
0.75	Intermediate Similarity	NPC261952
0.75	Intermediate Similarity	NPC169511
0.75	Intermediate Similarity	NPC473905
0.75	Intermediate Similarity	NPC320458
0.7473	Intermediate Similarity	NPC256368
0.7473	Intermediate Similarity	NPC474035
0.7473	Intermediate Similarity	NPC81386
0.7473	Intermediate Similarity	NPC472467
0.7471	Intermediate Similarity	NPC114694
0.7471	Intermediate Similarity	NPC474949
0.7471	Intermediate Similarity	NPC142117
0.7471	Intermediate Similarity	NPC475019
0.7471	Intermediate Similarity	NPC473840
0.7471	Intermediate Similarity	NPC231096
0.7471	Intermediate Similarity	NPC240695
0.7471	Intermediate Similarity	NPC219652
0.7471	Intermediate Similarity	NPC62118
0.7471	Intermediate Similarity	NPC25703
0.7471	Intermediate Similarity	NPC282815
0.7471	Intermediate Similarity	NPC171174
0.7471	Intermediate Similarity	NPC232555
0.7471	Intermediate Similarity	NPC107717
0.7471	Intermediate Similarity	NPC475581
0.7468	Intermediate Similarity	NPC477087
0.7468	Intermediate Similarity	NPC477086
0.7442	Intermediate Similarity	NPC186155
0.7442	Intermediate Similarity	NPC78673
0.7442	Intermediate Similarity	NPC474780
0.7442	Intermediate Similarity	NPC160517
0.7442	Intermediate Similarity	NPC163093
0.7439	Intermediate Similarity	NPC477203
0.7436	Intermediate Similarity	NPC101622
0.7416	Intermediate Similarity	NPC40066
0.7416	Intermediate Similarity	NPC93794
0.7416	Intermediate Similarity	NPC42598
0.7416	Intermediate Similarity	NPC91067
0.7416	Intermediate Similarity	NPC20621
0.7416	Intermediate Similarity	NPC81778
0.7416	Intermediate Similarity	NPC318963
0.7416	Intermediate Similarity	NPC473504
0.7412	Intermediate Similarity	NPC475159
0.7412	Intermediate Similarity	NPC473712
0.7412	Intermediate Similarity	NPC145914
0.7412	Intermediate Similarity	NPC473780
0.7412	Intermediate Similarity	NPC473529
0.7412	Intermediate Similarity	NPC11332
0.7412	Intermediate Similarity	NPC131002
0.7412	Intermediate Similarity	NPC94875
0.7412	Intermediate Similarity	NPC180363
0.7412	Intermediate Similarity	NPC65930
0.7412	Intermediate Similarity	NPC329829
0.7412	Intermediate Similarity	NPC73310
0.7407	Intermediate Similarity	NPC217725
0.7407	Intermediate Similarity	NPC113639
0.7407	Intermediate Similarity	NPC12696
0.7391	Intermediate Similarity	NPC476720
0.7391	Intermediate Similarity	NPC270013
0.7391	Intermediate Similarity	NPC14961
0.7386	Intermediate Similarity	NPC473649
0.7386	Intermediate Similarity	NPC154097
0.7386	Intermediate Similarity	NPC473995
0.7386	Intermediate Similarity	NPC159750
0.7386	Intermediate Similarity	NPC470401
0.7381	Intermediate Similarity	NPC474739
0.7381	Intermediate Similarity	NPC200446
0.7363	Intermediate Similarity	NPC320089
0.7356	Intermediate Similarity	NPC47958
0.7356	Intermediate Similarity	NPC477013
0.7356	Intermediate Similarity	NPC477018
0.7356	Intermediate Similarity	NPC132496
0.7356	Intermediate Similarity	NPC304509
0.7356	Intermediate Similarity	NPC473651
0.7356	Intermediate Similarity	NPC223871
0.7356	Intermediate Similarity	NPC477746
0.7356	Intermediate Similarity	NPC1083
0.7356	Intermediate Similarity	NPC477747
0.7356	Intermediate Similarity	NPC66346
0.7356	Intermediate Similarity	NPC82795
0.7356	Intermediate Similarity	NPC477014
0.7356	Intermediate Similarity	NPC110710
0.7356	Intermediate Similarity	NPC329749
0.7356	Intermediate Similarity	NPC231009
0.7356	Intermediate Similarity	NPC100921
0.7356	Intermediate Similarity	NPC286338
0.7356	Intermediate Similarity	NPC137033
0.7356	Intermediate Similarity	NPC473669
0.7356	Intermediate Similarity	NPC283085
0.7356	Intermediate Similarity	NPC103284
0.7356	Intermediate Similarity	NPC149725
0.7356	Intermediate Similarity	NPC107986
0.7356	Intermediate Similarity	NPC473478
0.7349	Intermediate Similarity	NPC477089

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC3852 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	153
0.1-0.2	2072
0.2-0.3	4099
0.3-0.4	2006
0.4-0.5	522
0.5-0.6	261
0.6-0.7	33
0.7-0.8	4
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7528	Intermediate Similarity	NPD7838	Discovery
0.7253	Intermediate Similarity	NPD7983	Approved
0.7143	Intermediate Similarity	NPD46	Approved
0.7143	Intermediate Similarity	NPD6698	Approved
0.7	Intermediate Similarity	NPD4250	Approved
0.7	Intermediate Similarity	NPD7899	Clinical (unspecified phase)
0.7	Intermediate Similarity	NPD4251	Approved
0.6889	Remote Similarity	NPD4249	Approved
0.6837	Remote Similarity	NPD5344	Discontinued
0.6804	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6778	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.6731	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.663	Remote Similarity	NPD7524	Approved
0.6629	Remote Similarity	NPD6435	Approved
0.6591	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6591	Remote Similarity	NPD4822	Approved
0.6591	Remote Similarity	NPD4819	Approved
0.6591	Remote Similarity	NPD4820	Approved
0.6591	Remote Similarity	NPD4821	Approved
0.6556	Remote Similarity	NPD7154	Phase 3
0.6556	Remote Similarity	NPD5362	Discontinued
0.6517	Remote Similarity	NPD5369	Approved
0.65	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.6484	Remote Similarity	NPD7338	Clinical (unspecified phase)
0.6476	Remote Similarity	NPD6371	Approved
0.6442	Remote Similarity	NPD6686	Approved
0.6413	Remote Similarity	NPD1733	Clinical (unspecified phase)
0.6404	Remote Similarity	NPD5368	Approved
0.64	Remote Similarity	NPD6648	Approved
0.6392	Remote Similarity	NPD5282	Discontinued
0.6375	Remote Similarity	NPD3197	Phase 1
0.6374	Remote Similarity	NPD5331	Approved
0.6374	Remote Similarity	NPD5332	Approved
0.6374	Remote Similarity	NPD6695	Phase 3
0.6364	Remote Similarity	NPD4268	Approved
0.6364	Remote Similarity	NPD4271	Approved
0.6333	Remote Similarity	NPD4790	Discontinued
0.6322	Remote Similarity	NPD6933	Approved
0.6316	Remote Similarity	NPD1695	Approved
0.63	Remote Similarity	NPD4225	Approved
0.63	Remote Similarity	NPD7638	Approved
0.6289	Remote Similarity	NPD5778	Approved
0.6289	Remote Similarity	NPD5779	Approved
0.6277	Remote Similarity	NPD7750	Discontinued
0.625	Remote Similarity	NPD8294	Approved
0.625	Remote Similarity	NPD8377	Approved
0.6238	Remote Similarity	NPD7640	Approved
0.6238	Remote Similarity	NPD7639	Approved
0.6216	Remote Similarity	NPD7328	Approved
0.6216	Remote Similarity	NPD7327	Approved
0.6195	Remote Similarity	NPD8378	Approved
0.6195	Remote Similarity	NPD8033	Approved
0.6195	Remote Similarity	NPD8379	Approved
0.6195	Remote Similarity	NPD8296	Approved
0.6195	Remote Similarity	NPD8335	Approved
0.6195	Remote Similarity	NPD8380	Approved
0.619	Remote Similarity	NPD6412	Phase 2
0.6186	Remote Similarity	NPD7637	Suspended
0.618	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6162	Remote Similarity	NPD1698	Clinical (unspecified phase)
0.6161	Remote Similarity	NPD7516	Approved
0.6154	Remote Similarity	NPD6109	Phase 1
0.6146	Remote Similarity	NPD6101	Approved
0.6146	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6129	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.6122	Remote Similarity	NPD6399	Phase 3
0.6122	Remote Similarity	NPD5781	Clinical (unspecified phase)
0.61	Remote Similarity	NPD7839	Suspended
0.6092	Remote Similarity	NPD6924	Approved
0.6092	Remote Similarity	NPD6926	Approved
0.6087	Remote Similarity	NPD4270	Approved
0.6087	Remote Similarity	NPD4269	Approved
0.6082	Remote Similarity	NPD3168	Discontinued
0.6055	Remote Similarity	NPD6053	Discontinued
0.6053	Remote Similarity	NPD8515	Approved
0.6053	Remote Similarity	NPD8516	Approved
0.6053	Remote Similarity	NPD8517	Approved
0.6053	Remote Similarity	NPD8513	Phase 3
0.6044	Remote Similarity	NPD7525	Registered
0.6044	Remote Similarity	NPD6930	Phase 2
0.6044	Remote Similarity	NPD6931	Approved
0.6022	Remote Similarity	NPD6110	Phase 1
0.602	Remote Similarity	NPD6411	Approved
0.6	Remote Similarity	NPD5786	Approved
0.6	Remote Similarity	NPD4632	Approved
0.6	Remote Similarity	NPD1145	Discontinued
0.5976	Remote Similarity	NPD7909	Approved
0.5941	Remote Similarity	NPD4792	Clinical (unspecified phase)
0.5934	Remote Similarity	NPD6929	Approved
0.5932	Remote Similarity	NPD8293	Discontinued
0.593	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.5926	Remote Similarity	NPD8132	Clinical (unspecified phase)
0.5926	Remote Similarity	NPD4061	Clinical (unspecified phase)
0.5926	Remote Similarity	NPD368	Approved
0.5913	Remote Similarity	NPD7503	Approved
0.5909	Remote Similarity	NPD8297	Approved
0.59	Remote Similarity	NPD7748	Approved
0.5897	Remote Similarity	NPD7492	Approved
0.5897	Remote Similarity	NPD2267	Suspended
0.5895	Remote Similarity	NPD5363	Approved
0.5889	Remote Similarity	NPD6932	Approved
0.5888	Remote Similarity	NPD6685	Approved
0.5882	Remote Similarity	NPD6084	Phase 2
0.5882	Remote Similarity	NPD6083	Phase 2
0.5882	Remote Similarity	NPD7736	Approved
0.5882	Remote Similarity	NPD7902	Approved
0.587	Remote Similarity	NPD7509	Discontinued
0.587	Remote Similarity	NPD4252	Approved
0.5859	Remote Similarity	NPD7087	Discontinued
0.5856	Remote Similarity	NPD8133	Approved
0.5847	Remote Similarity	NPD6616	Approved
0.5847	Remote Similarity	NPD7507	Approved
0.5843	Remote Similarity	NPD8039	Approved
0.5841	Remote Similarity	NPD8137	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD7331	Phase 2
0.5833	Remote Similarity	NPD7320	Approved
0.5826	Remote Similarity	NPD6059	Approved
0.5826	Remote Similarity	NPD6054	Approved
0.5826	Remote Similarity	NPD6319	Approved
0.5816	Remote Similarity	NPD6051	Approved
0.581	Remote Similarity	NPD3653	Clinical (unspecified phase)
0.5802	Remote Similarity	NPD4246	Clinical (unspecified phase)
0.5798	Remote Similarity	NPD7078	Approved
0.5798	Remote Similarity	NPD8074	Phase 3
0.5794	Remote Similarity	NPD6008	Approved
0.5794	Remote Similarity	NPD6675	Approved
0.5794	Remote Similarity	NPD7128	Approved
0.5794	Remote Similarity	NPD5739	Approved
0.5794	Remote Similarity	NPD6402	Approved
0.5765	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.5761	Remote Similarity	NPD6683	Phase 2
0.5758	Remote Similarity	NPD5785	Approved
0.5729	Remote Similarity	NPD6893	Approved
0.5726	Remote Similarity	NPD6370	Approved
0.5714	Remote Similarity	NPD8273	Phase 1
0.5714	Remote Similarity	NPD5776	Phase 2
0.5714	Remote Similarity	NPD6925	Approved
0.5714	Remote Similarity	NPD6903	Approved
0.5702	Remote Similarity	NPD6009	Approved
0.5702	Remote Similarity	NPD7319	Approved
0.5702	Remote Similarity	NPD7505	Discontinued
0.57	Remote Similarity	NPD7515	Phase 2
0.57	Remote Similarity	NPD8034	Phase 2
0.57	Remote Similarity	NPD8035	Phase 2
0.5699	Remote Similarity	NPD7332	Phase 2
0.5699	Remote Similarity	NPD7514	Phase 3
0.5688	Remote Similarity	NPD6881	Approved
0.5688	Remote Similarity	NPD6899	Approved
0.5688	Remote Similarity	NPD5345	Clinical (unspecified phase)
0.5686	Remote Similarity	NPD5695	Phase 3
0.5678	Remote Similarity	NPD8328	Phase 3
0.5678	Remote Similarity	NPD7604	Phase 2
0.5676	Remote Similarity	NPD8130	Phase 1
0.567	Remote Similarity	NPD5330	Approved
0.567	Remote Similarity	NPD7521	Approved
0.567	Remote Similarity	NPD7146	Approved
0.567	Remote Similarity	NPD7334	Approved
0.567	Remote Similarity	NPD6409	Approved
0.567	Remote Similarity	NPD6684	Approved
0.567	Remote Similarity	NPD6422	Discontinued
0.5667	Remote Similarity	NPD6942	Approved
0.5667	Remote Similarity	NPD7339	Approved
0.566	Remote Similarity	NPD7632	Discontinued
0.5657	Remote Similarity	NPD5370	Suspended
0.5652	Remote Similarity	NPD7641	Discontinued
0.5652	Remote Similarity	NPD7145	Approved
0.5648	Remote Similarity	NPD5357	Phase 1
0.5641	Remote Similarity	NPD3194	Approved
0.5641	Remote Similarity	NPD3196	Approved
0.5641	Remote Similarity	NPD3730	Approved
0.5641	Remote Similarity	NPD3195	Phase 2
0.5641	Remote Similarity	NPD6015	Approved
0.5641	Remote Similarity	NPD3728	Approved
0.5641	Remote Similarity	NPD4266	Approved
0.5641	Remote Similarity	NPD8274	Clinical (unspecified phase)
0.5641	Remote Similarity	NPD5983	Phase 2
0.5641	Remote Similarity	NPD6016	Approved
0.5638	Remote Similarity	NPD6898	Phase 1
0.5636	Remote Similarity	NPD6372	Approved
0.5636	Remote Similarity	NPD6373	Approved
0.5632	Remote Similarity	NPD6922	Approved
0.5632	Remote Similarity	NPD6923	Approved
0.563	Remote Similarity	NPD8341	Approved
0.563	Remote Similarity	NPD8340	Approved
0.563	Remote Similarity	NPD8342	Approved
0.563	Remote Similarity	NPD8299	Approved
0.5625	Remote Similarity	NPD4786	Approved
0.5607	Remote Similarity	NPD5765	Approved
0.5604	Remote Similarity	NPD3701	Clinical (unspecified phase)
0.56	Remote Similarity	NPD8522	Clinical (unspecified phase)

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data