NPASS Compound

Structure

NPC85803 OpenBabel06302216152D 29 33 0 0 1 0 0 0 0 0999 V2000 1.6332 -2.8768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6330 -1.8850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4491 -1.4136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4489 -0.4711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3078 0.0250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6326 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8165 -0.4714 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8163 0.4720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8167 -1.4139 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0004 -1.8853 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8158 -1.4142 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8160 -0.4717 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3488 0.0223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2948 0.7469 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6946 1.1564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8427 2.1371 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0002 0.9425 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6327 0.9422 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2999 1.6091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6325 -0.0003 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4488 -0.4720 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4487 -1.4145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2656 -1.8864 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6322 -1.8856 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2660 -0.0005 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4495 0.4714 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8872 1.2627 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6324 0.9918 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 9 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 6 29 1 0 0 0 0 7 27 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 24 1 0 0 0 0 12 27 1 0 0 0 0 12 13 1 0 0 0 0 12 20 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 17 27 1 0 0 0 0 17 28 1 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 20 26 1 0 0 0 0 21 22 1 0 0 0 0 21 25 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	472.36
Volume:	514.542
LogP:	4.884
LogD:	3.782
LogS:	-4.288
# Rotatable Bonds:	2
TPSA:	77.76
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.418
Synthetic Accessibility Score:	4.847
Fsp3:	0.9
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.329
MDCK Permeability:	1.6555513866478577e-05
Pgp-inhibitor:	0.012
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.025
30% Bioavailability (F30%):	0.28

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.578
Plasma Protein Binding (PPB):	93.56491088867188%
Volume Distribution (VD):	0.61
Pgp-substrate:	6.32802677154541%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.28
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.808
CYP2C9-inhibitor:	0.019
CYP2C9-substrate:	0.049
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.057
CYP3A4-inhibitor:	0.312
CYP3A4-substrate:	0.196

ADMET: Excretion

Clearance (CL):	2.593
Half-life (T1/2):	0.214

ADMET: Toxicity

hERG Blockers:	0.051
Human Hepatotoxicity (H-HT):	0.401
Drug-inuced Liver Injury (DILI):	0.022
AMES Toxicity:	0.017
Rat Oral Acute Toxicity:	0.628
Maximum Recommended Daily Dose:	0.963
Skin Sensitization:	0.857
Carcinogencity:	0.409
Eye Corrosion:	0.128
Eye Irritation:	0.117
Respiratory Toxicity:	0.971

Download Data

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

Natural Product: NPC85803

Natural Product ID:	NPC85803
*Common Name:**	HMYJDAYRUWUUAU-PSRPUKNFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HMYJDAYRUWUUAU-PSRPUKNFSA-N
Standard InCHI:	InChI=1S/C20H24O9/c1-7-4-10(21)12(22)17(3)9(7)5-11-18-6-28-16(25)19(26,15(17)18)8(2)20(18,27)13(23)14(24)29-11/h4,8-9,11-13,15,22-23,26-27H,5-6H2,1-3H3/t8-,9-,11-,12-,13+,15-,17-,18-,19-,20+/m1/s1
SMILES:	CC1=CC(=O)[C@H]([C@@]2(C)[C@@H]1C[C@@H]1[C@]34COC(=O)[C@@]([C@@H](C)[C@@]4([C@H](C(=O)O1)O)O)([C@H]23)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001640] Naphthopyrans

*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	n.a.	n.a.	n.a.	PMID[19299148]
NPO9965	Eurycoma longifolia	Species	Simaroubaceae	Eukaryota	roots	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]
NPO14602	Vitex negundo	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
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]
NPO893	Helichrysum sutherlandii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
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]
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]
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]
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]
NPO9024	Aralidium pinnatifidum	Species	Torricelliaceae	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]
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]
NPO6014	Goniothalamus undulatus	Species	Annonaceae	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]
NPO14280	Helichrysum angustifolium	Species	Asteraceae	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC85803 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	255
0.1-0.2	1517
0.2-0.3	4817
0.3-0.4	8176
0.4-0.5	11827
0.5-0.6	6397
0.6-0.7	5331
0.7-0.8	3653
0.8-0.85	561
0.85-0.9	136
0.9-0.95	26
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID

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 NPC85803 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	221
0.1-0.2	1772
0.2-0.3	3914
0.3-0.4	2056
0.4-0.5	653
0.5-0.6	239
0.6-0.7	126
0.7-0.8	118
0.8-0.85	41
0.85-0.9	10
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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