NPASS Compound

Structure

CID38893 OpenBabel06191715372D 22 24 0 0 1 0 0 0 0 0999 V2000 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 12 1 0 0 0 0 2 12 1 0 0 0 0 3 19 1 0 0 0 0 4 19 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 7 19 1 0 0 0 0 8 20 1 0 0 0 0 9 13 2 0 0 0 0 9 14 1 0 0 0 0 10 13 1 0 0 0 0 10 17 1 0 0 0 0 11 15 2 0 0 0 0 11 16 1 0 0 0 0 12 14 1 0 0 0 0 13 15 1 0 0 0 0 14 16 2 0 0 0 0 15 20 1 0 0 0 0 16 21 1 0 0 0 0 17 18 1 0 0 0 0 17 22 1 1 0 0 0 18 19 1 0 0 0 0 18 20 1 1 0 0 0 20 5 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	302.22
Volume:	338.478
LogP:	5.097
LogD:	4.291
LogS:	-5.285
# Rotatable Bonds:	1
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.801
Synthetic Accessibility Score:	3.849
Fsp3:	0.7
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.742
MDCK Permeability:	1.6762949599069543e-05
Pgp-inhibitor:	0.944
Pgp-substrate:	0.02
Human Intestinal Absorption (HIA):	0.023
20% Bioavailability (F20%):	0.997
30% Bioavailability (F30%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.346
Plasma Protein Binding (PPB):	96.74830627441406%
Volume Distribution (VD):	2.852
Pgp-substrate:	4.290327072143555%

ADMET: Metabolism

CYP1A2-inhibitor:	0.225
CYP1A2-substrate:	0.848
CYP2C19-inhibitor:	0.386
CYP2C19-substrate:	0.889
CYP2C9-inhibitor:	0.304
CYP2C9-substrate:	0.912
CYP2D6-inhibitor:	0.638
CYP2D6-substrate:	0.643
CYP3A4-inhibitor:	0.395
CYP3A4-substrate:	0.507

ADMET: Excretion

Clearance (CL):	10.321
Half-life (T1/2):	0.104

ADMET: Toxicity

hERG Blockers:	0.032
Human Hepatotoxicity (H-HT):	0.111
Drug-inuced Liver Injury (DILI):	0.099
AMES Toxicity:	0.032
Rat Oral Acute Toxicity:	0.522
Maximum Recommended Daily Dose:	0.902
Skin Sensitization:	0.774
Carcinogencity:	0.059
Eye Corrosion:	0.005
Eye Irritation:	0.731
Respiratory Toxicity:	0.912

Download Data

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

Natural Product: NPC38893

Natural Product ID:	NPC38893
*Common Name:**	(4Bs,8As,9R)-4B,8,8-Trimethyl-2-Propan-2-Yl-5,6,7,8A,9,10-Hexahydrophenanthrene-3,9-Diol
IUPAC Name:	(4bS,8aS,9R)-4b,8,8-trimethyl-2-propan-2-yl-5,6,7,8a,9,10-hexahydrophenanthrene-3,9-diol
Synonyms:
Standard InCHIKey:	XEJHUBFVQWSNJW-WSTZPKSXSA-N
Standard InCHI:	InChI=1S/C20H30O2/c1-12(2)14-9-13-10-17(22)18-19(3,4)7-6-8-20(18,5)15(13)11-16(14)21/h9,11-12,17-18,21-22H,6-8,10H2,1-5H3/t17-,18+,20-/m1/s1
SMILES:	CC(C)c1cc2C[C@H]([C@H]3C(C)(C)CCC[C@]3(C)c2cc1O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1094422
PubChem CID:	14378752
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO13135	Campylotropis hirtella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19481938]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28294615]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31291099]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13135	Campylotropis hirtella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6731	Ononis spinosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7773	Crinum moorei	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6731	Ononis spinosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7773	Crinum moorei	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13135	Campylotropis hirtella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6731	Ononis spinosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO7773	Crinum moorei	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1815	Breonia chinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1257	Distephanus angulifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9704	Sonneratia caseolaris	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23384	Rhodiola semenovii	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9319	Pterocaulon virgatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21720	Talaromyces variabilis	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10638	Plectranthus myrianthus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7822.1	Eucalyptus globulus subsp. bicostata	Subspecies	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3873	Crotalaria candicans	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11843	Stephania zippeliana	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12091	Martensia denticulata	Species	Delesseriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12565	Hypericum polyanthemum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO526	Salvia sessei	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11190	Veronica polita	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6731	Ononis spinosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10922	Pentaclethra macrophylla	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12205	Eucalyptus apodophylla	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5043	Eria japonica	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8934	Gypsophila perfoliata	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11576	Glycosmis macrophylla	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9532	Vernonia cistifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10605	Tristania conferta	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13135	Campylotropis hirtella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22691	Mentha cardiaca	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6289	Ceropegia dichotoma	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5456	Juniperus drupacea	Species	Cupressaceae	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
MIC	2

Activity Type	# Activity
Organism	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	4.0	ug.mL-1	PMID[547087]
NPT1605	Organism	Enterococcus	Enterococcus	MIC	=	4.0	ug.mL-1	PMID[547087]

☑ 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 NPC38893 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	279
0.1-0.2	1461
0.2-0.3	3028
0.3-0.4	9088
0.4-0.5	10402
0.5-0.6	10196
0.6-0.7	6483
0.7-0.8	1481
0.8-0.85	158
0.85-0.9	79
0.9-0.95	21
0.95-1	21

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC308311
1.0	High Similarity	NPC477137
0.9907	High Similarity	NPC192948
0.9907	High Similarity	NPC35797
0.9818	High Similarity	NPC471671
0.9817	High Similarity	NPC219112
0.973	High Similarity	NPC469644
0.9727	High Similarity	NPC172219
0.9727	High Similarity	NPC304510
0.9727	High Similarity	NPC477136
0.9725	High Similarity	NPC147179
0.9636	High Similarity	NPC92
0.9636	High Similarity	NPC469663
0.9636	High Similarity	NPC308828
0.9633	High Similarity	NPC268160
0.9537	High Similarity	NPC176279
0.9537	High Similarity	NPC260323
0.9464	High Similarity	NPC469609
0.9464	High Similarity	NPC154030
0.9286	High Similarity	NPC471668
0.9279	High Similarity	NPC195922
0.9273	High Similarity	NPC250323
0.9273	High Similarity	NPC228425
0.9266	High Similarity	NPC132720
0.9266	High Similarity	NPC141782
0.9231	High Similarity	NPC181334
0.9167	High Similarity	NPC151477
0.9145	High Similarity	NPC471187
0.913	High Similarity	NPC260832
0.913	High Similarity	NPC135467
0.9123	High Similarity	NPC164649
0.9123	High Similarity	NPC48342
0.9099	High Similarity	NPC46940
0.9091	High Similarity	NPC13482
0.906	High Similarity	NPC11250
0.906	High Similarity	NPC471794
0.9052	High Similarity	NPC328504
0.9043	High Similarity	NPC93071
0.9043	High Similarity	NPC126002
0.9018	High Similarity	NPC715
0.9009	High Similarity	NPC95716
0.9	High Similarity	NPC471077
0.8981	High Similarity	NPC117115
0.8947	High Similarity	NPC137496
0.8947	High Similarity	NPC474387
0.8947	High Similarity	NPC154511
0.8947	High Similarity	NPC474358
0.8947	High Similarity	NPC257540
0.8947	High Similarity	NPC247858
0.8917	High Similarity	NPC321822
0.8917	High Similarity	NPC325294
0.8909	High Similarity	NPC11554
0.8899	High Similarity	NPC21594
0.8898	High Similarity	NPC152946
0.8898	High Similarity	NPC71094
0.8879	High Similarity	NPC151197
0.887	High Similarity	NPC16030
0.886	High Similarity	NPC469719
0.8839	High Similarity	NPC151537
0.8839	High Similarity	NPC77772
0.8839	High Similarity	NPC322753
0.8833	High Similarity	NPC137750
0.8833	High Similarity	NPC76119
0.8833	High Similarity	NPC124030
0.8833	High Similarity	NPC87985
0.8833	High Similarity	NPC4286
0.8829	High Similarity	NPC58865
0.8824	High Similarity	NPC198014
0.8818	High Similarity	NPC27252
0.8818	High Similarity	NPC472979
0.8814	High Similarity	NPC249340
0.8814	High Similarity	NPC253627
0.8814	High Similarity	NPC142198
0.8814	High Similarity	NPC162935
0.8814	High Similarity	NPC77569
0.8807	High Similarity	NPC243601
0.876	High Similarity	NPC100414
0.876	High Similarity	NPC43000
0.8739	High Similarity	NPC321402
0.8739	High Similarity	NPC149455
0.8739	High Similarity	NPC64642
0.8739	High Similarity	NPC478058
0.8739	High Similarity	NPC472982
0.8729	High Similarity	NPC32322
0.8729	High Similarity	NPC259703
0.8689	High Similarity	NPC108164
0.8689	High Similarity	NPC186889
0.8684	High Similarity	NPC317869
0.8673	High Similarity	NPC470770
0.8673	High Similarity	NPC266937
0.8661	High Similarity	NPC314187
0.8655	High Similarity	NPC154696
0.8649	High Similarity	NPC472980
0.8644	High Similarity	NPC68339
0.8632	High Similarity	NPC206
0.8621	High Similarity	NPC141001
0.8611	High Similarity	NPC211885
0.8609	High Similarity	NPC471534
0.8596	High Similarity	NPC471179
0.8596	High Similarity	NPC302371
0.8596	High Similarity	NPC177962
0.8596	High Similarity	NPC62867
0.8583	High Similarity	NPC121168
0.8583	High Similarity	NPC176208
0.8571	High Similarity	NPC262365
0.8571	High Similarity	NPC241001
0.8571	High Similarity	NPC78307
0.856	High Similarity	NPC312341
0.856	High Similarity	NPC471851
0.8559	High Similarity	NPC271274
0.8559	High Similarity	NPC323074
0.8547	High Similarity	NPC299180
0.8545	High Similarity	NPC475225
0.8537	High Similarity	NPC476536
0.8534	High Similarity	NPC474486
0.8522	High Similarity	NPC322239
0.85	High Similarity	NPC475166
0.8492	Intermediate Similarity	NPC85595
0.8492	Intermediate Similarity	NPC321086
0.8487	Intermediate Similarity	NPC325544
0.8487	Intermediate Similarity	NPC477037
0.8487	Intermediate Similarity	NPC318581
0.8487	Intermediate Similarity	NPC478121
0.8482	Intermediate Similarity	NPC320439
0.848	Intermediate Similarity	NPC196193
0.8455	Intermediate Similarity	NPC19856
0.8455	Intermediate Similarity	NPC235762
0.8455	Intermediate Similarity	NPC471228
0.8455	Intermediate Similarity	NPC71610
0.844	Intermediate Similarity	NPC225506
0.8435	Intermediate Similarity	NPC473521
0.843	Intermediate Similarity	NPC297057
0.8425	Intermediate Similarity	NPC227719
0.8421	Intermediate Similarity	NPC44732
0.8421	Intermediate Similarity	NPC296683
0.8413	Intermediate Similarity	NPC476847
0.8403	Intermediate Similarity	NPC42657
0.8387	Intermediate Similarity	NPC84672
0.8387	Intermediate Similarity	NPC262936
0.8387	Intermediate Similarity	NPC69424
0.8387	Intermediate Similarity	NPC176130
0.8387	Intermediate Similarity	NPC30491
0.8387	Intermediate Similarity	NPC78364
0.8378	Intermediate Similarity	NPC272029
0.8378	Intermediate Similarity	NPC238696
0.8376	Intermediate Similarity	NPC84999
0.8376	Intermediate Similarity	NPC246760
0.8364	Intermediate Similarity	NPC252105
0.8362	Intermediate Similarity	NPC319803
0.8362	Intermediate Similarity	NPC263753
0.8359	Intermediate Similarity	NPC202225
0.8349	Intermediate Similarity	NPC33675
0.8349	Intermediate Similarity	NPC122005
0.8349	Intermediate Similarity	NPC299762
0.8349	Intermediate Similarity	NPC252821
0.8349	Intermediate Similarity	NPC128723
0.8348	Intermediate Similarity	NPC308689
0.8348	Intermediate Similarity	NPC469912
0.8347	Intermediate Similarity	NPC474115
0.8346	Intermediate Similarity	NPC165612
0.8346	Intermediate Similarity	NPC59239
0.8333	Intermediate Similarity	NPC99734
0.8333	Intermediate Similarity	NPC99795
0.8333	Intermediate Similarity	NPC318552
0.8333	Intermediate Similarity	NPC103916
0.8333	Intermediate Similarity	NPC190501
0.8333	Intermediate Similarity	NPC249425
0.832	Intermediate Similarity	NPC3009
0.832	Intermediate Similarity	NPC201069
0.8319	Intermediate Similarity	NPC66834
0.8308	Intermediate Similarity	NPC475957
0.8306	Intermediate Similarity	NPC470724
0.8305	Intermediate Similarity	NPC312105
0.8304	Intermediate Similarity	NPC138942
0.8304	Intermediate Similarity	NPC99557
0.8304	Intermediate Similarity	NPC219286
0.8304	Intermediate Similarity	NPC47284
0.8291	Intermediate Similarity	NPC107240
0.8291	Intermediate Similarity	NPC249270
0.8291	Intermediate Similarity	NPC12656
0.8288	Intermediate Similarity	NPC168829
0.8288	Intermediate Similarity	NPC269212
0.8281	Intermediate Similarity	NPC477139
0.8281	Intermediate Similarity	NPC49742
0.8273	Intermediate Similarity	NPC72729
0.8273	Intermediate Similarity	NPC174911
0.8273	Intermediate Similarity	NPC294741
0.8268	Intermediate Similarity	NPC78575
0.8268	Intermediate Similarity	NPC291001
0.8264	Intermediate Similarity	NPC129176
0.8261	Intermediate Similarity	NPC224870
0.8257	Intermediate Similarity	NPC6597
0.8257	Intermediate Similarity	NPC79241
0.8257	Intermediate Similarity	NPC77492
0.8254	Intermediate Similarity	NPC276238
0.825	Intermediate Similarity	NPC176893
0.8241	Intermediate Similarity	NPC144682
0.8241	Intermediate Similarity	NPC222146
0.824	Intermediate Similarity	NPC72667
0.8231	Intermediate Similarity	NPC68292

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 NPC38893 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	273
0.1-0.2	933
0.2-0.3	1328
0.3-0.4	2836
0.4-0.5	2028
0.5-0.6	1226
0.6-0.7	420
0.7-0.8	94
0.8-0.85	10
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9123	High Similarity	NPD3091	Approved
0.8814	High Similarity	NPD3092	Approved
0.8644	High Similarity	NPD3095	Discontinued
0.8525	High Similarity	NPD3094	Phase 2
0.8482	Intermediate Similarity	NPD2342	Discontinued
0.8435	Intermediate Similarity	NPD7635	Approved
0.8333	Intermediate Similarity	NPD4059	Approved
0.8333	Intermediate Similarity	NPD3019	Approved
0.8241	Intermediate Similarity	NPD1809	Phase 2
0.824	Intermediate Similarity	NPD5736	Approved
0.8182	Intermediate Similarity	NPD2932	Approved
0.8182	Intermediate Similarity	NPD3020	Approved
0.8165	Intermediate Similarity	NPD288	Approved
0.8073	Intermediate Similarity	NPD844	Approved
0.8062	Intermediate Similarity	NPD3619	Clinical (unspecified phase)
0.8062	Intermediate Similarity	NPD3620	Phase 2
0.8017	Intermediate Similarity	NPD4750	Phase 3
0.7984	Intermediate Similarity	NPD6663	Approved
0.7982	Intermediate Similarity	NPD1432	Clinical (unspecified phase)
0.7946	Intermediate Similarity	NPD289	Clinical (unspecified phase)
0.7939	Intermediate Similarity	NPD4097	Suspended
0.792	Intermediate Similarity	NPD3600	Clinical (unspecified phase)
0.7909	Intermediate Similarity	NPD2859	Approved
0.7909	Intermediate Similarity	NPD2860	Approved
0.7899	Intermediate Similarity	NPD7159	Clinical (unspecified phase)
0.789	Intermediate Similarity	NPD845	Approved
0.7886	Intermediate Similarity	NPD2286	Discontinued
0.7881	Intermediate Similarity	NPD6124	Clinical (unspecified phase)
0.7863	Intermediate Similarity	NPD3022	Approved
0.7863	Intermediate Similarity	NPD3021	Approved
0.782	Intermediate Similarity	NPD7743	Approved
0.782	Intermediate Similarity	NPD7742	Approved
0.7818	Intermediate Similarity	NPD2933	Approved
0.7818	Intermediate Similarity	NPD2934	Approved
0.7807	Intermediate Similarity	NPD5700	Clinical (unspecified phase)
0.7805	Intermediate Similarity	NPD4093	Discontinued
0.7786	Intermediate Similarity	NPD4140	Approved
0.7778	Intermediate Similarity	NPD5327	Phase 3
0.776	Intermediate Similarity	NPD5350	Clinical (unspecified phase)
0.776	Intermediate Similarity	NPD5351	Clinical (unspecified phase)
0.775	Intermediate Similarity	NPD4869	Clinical (unspecified phase)
0.7742	Intermediate Similarity	NPD4626	Approved
0.7742	Intermediate Similarity	NPD1751	Approved
0.7734	Intermediate Similarity	NPD4624	Approved
0.7734	Intermediate Similarity	NPD6917	Clinical (unspecified phase)
0.7727	Intermediate Similarity	NPD5735	Approved
0.768	Intermediate Similarity	NPD3026	Approved
0.768	Intermediate Similarity	NPD3023	Approved
0.7661	Intermediate Similarity	NPD3024	Approved
0.7661	Intermediate Similarity	NPD3025	Approved
0.7634	Intermediate Similarity	NPD6410	Clinical (unspecified phase)
0.7615	Intermediate Similarity	NPD2606	Approved
0.7615	Intermediate Similarity	NPD2605	Approved
0.7591	Intermediate Similarity	NPD3638	Discontinued
0.7561	Intermediate Similarity	NPD7325	Clinical (unspecified phase)
0.7557	Intermediate Similarity	NPD5155	Approved
0.7557	Intermediate Similarity	NPD5156	Approved
0.7538	Intermediate Similarity	NPD3635	Approved
0.7538	Intermediate Similarity	NPD3636	Approved
0.7538	Intermediate Similarity	NPD3637	Approved
0.7537	Intermediate Similarity	NPD6353	Approved
0.752	Intermediate Similarity	NPD5691	Approved
0.7519	Intermediate Similarity	NPD4060	Phase 1
0.7482	Intermediate Similarity	NPD7910	Clinical (unspecified phase)
0.7481	Intermediate Similarity	NPD3595	Approved
0.7481	Intermediate Similarity	NPD3594	Approved
0.7462	Intermediate Similarity	NPD2194	Approved
0.7462	Intermediate Similarity	NPD2195	Approved
0.746	Intermediate Similarity	NPD4589	Approved
0.7442	Intermediate Similarity	NPD6696	Suspended
0.7424	Intermediate Similarity	NPD4625	Phase 3
0.7417	Intermediate Similarity	NPD1792	Phase 2
0.7414	Intermediate Similarity	NPD846	Approved
0.7414	Intermediate Similarity	NPD940	Approved
0.7405	Intermediate Similarity	NPD2861	Phase 2
0.7398	Intermediate Similarity	NPD497	Approved
0.7368	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.7344	Intermediate Similarity	NPD1201	Approved
0.7338	Intermediate Similarity	NPD5698	Clinical (unspecified phase)
0.7324	Intermediate Similarity	NPD3645	Discontinued
0.7323	Intermediate Similarity	NPD5238	Clinical (unspecified phase)
0.7317	Intermediate Similarity	NPD2234	Approved
0.7317	Intermediate Similarity	NPD2229	Approved
0.7317	Intermediate Similarity	NPD2228	Approved
0.7317	Intermediate Similarity	NPD495	Approved
0.7317	Intermediate Similarity	NPD496	Approved
0.7317	Intermediate Similarity	NPD498	Approved
0.7308	Intermediate Similarity	NPD1283	Approved
0.7302	Intermediate Similarity	NPD5303	Approved
0.7302	Intermediate Similarity	NPD5304	Approved
0.7286	Intermediate Similarity	NPD7003	Approved
0.728	Intermediate Similarity	NPD7340	Approved
0.7254	Intermediate Similarity	NPD7041	Phase 2
0.7254	Intermediate Similarity	NPD7040	Clinical (unspecified phase)
0.7252	Intermediate Similarity	NPD4339	Clinical (unspecified phase)
0.7244	Intermediate Similarity	NPD1651	Approved
0.7231	Intermediate Similarity	NPD4749	Approved
0.7218	Intermediate Similarity	NPD4908	Phase 1
0.7214	Intermediate Similarity	NPD6674	Discontinued
0.7206	Intermediate Similarity	NPD3657	Discovery
0.7203	Intermediate Similarity	NPD4160	Clinical (unspecified phase)
0.7203	Intermediate Similarity	NPD7422	Clinical (unspecified phase)
0.7194	Intermediate Similarity	NPD4721	Approved
0.7194	Intermediate Similarity	NPD4726	Approved
0.7194	Intermediate Similarity	NPD4725	Approved
0.7179	Intermediate Similarity	NPD1242	Phase 1
0.7177	Intermediate Similarity	NPD1398	Phase 1
0.7174	Intermediate Similarity	NPD1509	Clinical (unspecified phase)
0.7167	Intermediate Similarity	NPD1444	Approved
0.7167	Intermediate Similarity	NPD1445	Approved
0.7165	Intermediate Similarity	NPD2226	Clinical (unspecified phase)
0.7165	Intermediate Similarity	NPD7330	Discontinued
0.7165	Intermediate Similarity	NPD7741	Discontinued
0.7163	Intermediate Similarity	NPD8166	Discontinued
0.7156	Intermediate Similarity	NPD111	Approved
0.7122	Intermediate Similarity	NPD5405	Approved
0.7122	Intermediate Similarity	NPD5406	Approved
0.7122	Intermediate Similarity	NPD5404	Approved
0.7122	Intermediate Similarity	NPD5408	Approved
0.7121	Intermediate Similarity	NPD1470	Approved
0.7109	Intermediate Similarity	NPD4235	Clinical (unspecified phase)
0.7109	Intermediate Similarity	NPD4196	Clinical (unspecified phase)
0.7099	Intermediate Similarity	NPD4659	Approved
0.7077	Intermediate Similarity	NPD1610	Phase 2
0.7077	Intermediate Similarity	NPD1281	Approved
0.7068	Intermediate Similarity	NPD6584	Phase 3
0.7063	Intermediate Similarity	NPD6671	Approved
0.7063	Intermediate Similarity	NPD7157	Approved
0.705	Intermediate Similarity	NPD3299	Clinical (unspecified phase)
0.7045	Intermediate Similarity	NPD8651	Approved
0.704	Intermediate Similarity	NPD5283	Phase 1
0.7034	Intermediate Similarity	NPD6273	Approved
0.7023	Intermediate Similarity	NPD2233	Approved
0.7023	Intermediate Similarity	NPD2230	Approved
0.7023	Intermediate Similarity	NPD2232	Approved
0.7021	Intermediate Similarity	NPD7037	Approved
0.7015	Intermediate Similarity	NPD4208	Discontinued
0.7014	Intermediate Similarity	NPD7390	Discontinued
0.7007	Intermediate Similarity	NPD2238	Phase 2
0.7	Intermediate Similarity	NPD6099	Approved
0.7	Intermediate Similarity	NPD3143	Discontinued
0.7	Intermediate Similarity	NPD6100	Approved
0.6993	Remote Similarity	NPD8131	Suspended
0.6992	Remote Similarity	NPD4103	Phase 2
0.6992	Remote Similarity	NPD4104	Clinical (unspecified phase)
0.6986	Remote Similarity	NPD5699	Approved
0.6985	Remote Similarity	NPD6812	Clinical (unspecified phase)
0.6984	Remote Similarity	NPD5951	Approved
0.6978	Remote Similarity	NPD7718	Clinical (unspecified phase)
0.697	Remote Similarity	NPD1669	Approved
0.695	Remote Similarity	NPD2029	Clinical (unspecified phase)
0.695	Remote Similarity	NPD5763	Approved
0.695	Remote Similarity	NPD5762	Approved
0.6934	Remote Similarity	NPD6407	Approved
0.6934	Remote Similarity	NPD8032	Phase 2
0.6934	Remote Similarity	NPD6405	Approved
0.6923	Remote Similarity	NPD7725	Approved
0.6917	Remote Similarity	NPD9500	Approved
0.6912	Remote Similarity	NPD3027	Phase 3
0.6911	Remote Similarity	NPD2684	Approved
0.6906	Remote Similarity	NPD4579	Clinical (unspecified phase)
0.6906	Remote Similarity	NPD2157	Approved
0.6897	Remote Similarity	NPD2420	Approved
0.6897	Remote Similarity	NPD2421	Approved
0.6894	Remote Similarity	NPD3070	Discontinued
0.6892	Remote Similarity	NPD5808	Clinical (unspecified phase)
0.6891	Remote Similarity	NPD3028	Approved
0.6884	Remote Similarity	NPD3109	Approved
0.6884	Remote Similarity	NPD2979	Phase 3
0.6884	Remote Similarity	NPD3110	Approved
0.688	Remote Similarity	NPD228	Approved
0.6875	Remote Similarity	NPD7636	Approved
0.687	Remote Similarity	NPD2688	Clinical (unspecified phase)
0.6866	Remote Similarity	NPD1131	Approved
0.6866	Remote Similarity	NPD1134	Approved
0.6866	Remote Similarity	NPD1133	Approved
0.6866	Remote Similarity	NPD1135	Approved
0.6866	Remote Similarity	NPD1129	Approved
0.6861	Remote Similarity	NPD7294	Phase 1
0.6855	Remote Similarity	NPD5451	Approved
0.6855	Remote Similarity	NPD9380	Clinical (unspecified phase)
0.685	Remote Similarity	NPD9618	Approved
0.685	Remote Similarity	NPD1793	Approved
0.685	Remote Similarity	NPD1791	Approved
0.685	Remote Similarity	NPD9614	Approved
0.685	Remote Similarity	NPD2629	Approved
0.6849	Remote Similarity	NPD7004	Clinical (unspecified phase)
0.6846	Remote Similarity	NPD1357	Approved
0.6842	Remote Similarity	NPD6582	Phase 2
0.6842	Remote Similarity	NPD6583	Phase 3
0.6818	Remote Similarity	NPD1611	Approved
0.6809	Remote Similarity	NPD1753	Discontinued
0.6809	Remote Similarity	NPD4108	Discontinued
0.6803	Remote Similarity	NPD6090	Discontinued
0.6797	Remote Similarity	NPD4198	Discontinued
0.6797	Remote Similarity	NPD709	Approved
0.6794	Remote Similarity	NPD5125	Phase 3
0.6794	Remote Similarity	NPD2667	Approved
0.6794	Remote Similarity	NPD1778	Approved
0.6794	Remote Similarity	NPD2668	Approved

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