NPASS Compound

Structure

CID97202 OpenBabel06191715432D 34 37 0 0 1 0 0 0 0 0999 V2000 -1.4276 -4.5185 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8552 -3.7296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5349 -0.5240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0006 -1.9862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2430 -3.3276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6897 -0.9756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6891 -0.9746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8331 -2.2619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7233 -2.6589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8446 -1.4632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6888 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8454 1.4633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3800 1.9504 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3795 -0.0010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6900 -0.0005 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8452 0.4876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5355 1.4628 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6906 1.9509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2243 1.4623 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2240 0.4866 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8454 -1.4627 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.0442 -2.8344 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8246 -3.6283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5352 0.4871 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0003 -0.9751 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8460 -2.4374 0.0000 C 0 0 1 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 -1.6909 2.9620 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1002 1.9675 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0996 -0.0190 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1455 -3.8038 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7148 -4.0253 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8154 -2.5387 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 23 1 0 0 0 0 2 23 1 0 0 0 0 4 25 1 0 0 0 0 6 10 1 0 0 0 0 6 15 1 0 0 0 0 7 11 1 0 0 0 0 7 21 1 0 0 0 0 8 9 1 0 0 0 0 8 22 1 0 0 0 0 9 23 1 0 0 0 0 10 25 1 0 0 0 0 11 27 1 0 0 0 0 12 16 2 0 0 0 0 12 18 1 0 0 0 0 13 17 1 0 0 0 0 13 19 1 0 0 0 0 14 20 1 0 0 0 0 14 24 1 0 0 0 0 15 16 1 0 0 0 0 15 24 1 0 0 0 0 16 27 1 0 0 0 0 17 18 1 0 0 0 0 17 24 1 1 0 0 0 18 28 2 0 0 0 0 19 20 1 0 0 0 0 19 29 1 6 0 0 0 20 30 1 6 0 0 0 21 25 1 0 0 0 0 21 26 1 0 0 0 0 22 26 1 0 0 0 0 22 31 1 6 0 0 0 23 32 1 0 0 0 0 24 3 1 6 0 0 0 25 27 1 6 0 0 0 26 5 1 6 0 0 0 26 33 1 0 0 0 0 27 34 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	480.31
Volume:	497.581
LogP:	1.252
LogD:	0.07
LogS:	-3.198
# Rotatable Bonds:	5
TPSA:	138.45
# H-Bond Aceptor:	7
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.331
Synthetic Accessibility Score:	5.338
Fsp3:	0.889
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:	-4.975
MDCK Permeability:	6.262155238800915e-06
Pgp-inhibitor:	0.006
Pgp-substrate:	0.856
Human Intestinal Absorption (HIA):	0.119
20% Bioavailability (F20%):	0.715
30% Bioavailability (F30%):	0.055

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.309
Plasma Protein Binding (PPB):	59.01949691772461%
Volume Distribution (VD):	0.706
Pgp-substrate:	22.640533447265625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.245
CYP2C19-inhibitor:	0.006
CYP2C19-substrate:	0.721
CYP2C9-inhibitor:	0.013
CYP2C9-substrate:	0.163
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.044
CYP3A4-inhibitor:	0.121
CYP3A4-substrate:	0.436

ADMET: Excretion

Clearance (CL):	2.636
Half-life (T1/2):	0.512

ADMET: Toxicity

hERG Blockers:	0.064
Human Hepatotoxicity (H-HT):	0.287
Drug-inuced Liver Injury (DILI):	0.041
AMES Toxicity:	0.118
Rat Oral Acute Toxicity:	0.454
Maximum Recommended Daily Dose:	0.937
Skin Sensitization:	0.355
Carcinogencity:	0.041
Eye Corrosion:	0.005
Eye Irritation:	0.049
Respiratory Toxicity:	0.954

Download Data

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

Natural Product: NPC97202

Natural Product ID:	NPC97202
*Common Name:**	(2S,3R,5R,10R,13R,14S)-2,3,14-Trihydroxy-10,13-Dimethyl-17-[(2R,3R)-2,3,6-Trihydroxy-6-Methylheptan-2-Yl]-2,3,4,5,9,11,12,15,16,17-Decahydro-1H-Cyclopenta[A]Phenanthren-6-One
IUPAC Name:	(2S,3R,5R,10R,13R,14S)-2,3,14-trihydroxy-10,13-dimethyl-17-[(2R,3R)-2,3,6-trihydroxy-6-methylheptan-2-yl]-2,3,4,5,9,11,12,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-6-one
Synonyms:
Standard InCHIKey:	NKDFYOWSKOHCCO-JWWMQFFDSA-N
Standard InCHI:	InChI=1S/C27H44O7/c1-23(2,32)9-8-22(31)26(5,33)21-7-11-27(34)16-12-18(28)17-13-19(29)20(30)14-24(17,3)15(16)6-10-25(21,27)4/h12,15,17,19-22,29-34H,6-11,13-14H2,1-5H3/t15?,17-,19+,20-,21?,22+,24+,25+,26+,27+/m0/s1
SMILES:	CC(C)(CC[C@H]([C@@](C)(C1CC[C@]2(C3=CC(=O)[C@@H]4C[C@H]([C@H](C[C@]4(C)C3CC[C@]12C)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1707235
PubChem CID:	44143979
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO17539	Ajuga decumbens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9748375]
NPO16818	Trillium tschonoskii	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32870000]
NPO9740	Dacrycarpus imbricatus	Species	Podocarpaceae	Eukaryota	Twigs	n.a.	n.a.	PMID[32786878]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	Root barks	n.a.	n.a.	PMID[3097265]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	latex	n.a.	PMID[27294120]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[25981820]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	leaves	Chungbuk, Korea	n.a.	PMID[25935644]
NPO16653	Matteuccia struthiopteris	Species	Onocleaceae	Eukaryota	rhizomes	Liaoning province, China	2011-SEP	PMID[25927664]
NPO29798	Podocarpus imbricatus	Species	Podocarpaceae	Eukaryota	twigs and leaves	n.a.	n.a.	PMID[24953598]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	root bark	University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic	2011-APR	PMID[24901948]

Showing 1 to 10 of 127 entries

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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
Potency	3

Activity Type	# Activity
Individual Protein	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT64	Individual Protein	ATPase family AAA domain-containing protein 5	Homo sapiens	Potency	n.a.	29081.0	nM	PMID[489801]
NPT10	Individual Protein	Geminin	Homo sapiens	Potency	n.a.	1032.3	nM	PMID[489801]
NPT8	Individual Protein	DNA polymerase iota	Homo sapiens	Potency	n.a.	10000.0	nM	PMID[489801]

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☑ 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 NPC97202 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	203
0.1-0.2	1288
0.2-0.3	4406
0.3-0.4	8636
0.4-0.5	12604
0.5-0.6	6549
0.6-0.7	5959
0.7-0.8	2698
0.8-0.85	258
0.85-0.9	52
0.9-0.95	16
0.95-1	28

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC49958
1.0	High Similarity	NPC48733
1.0	High Similarity	NPC296945
1.0	High Similarity	NPC50692
1.0	High Similarity	NPC319077

Showing 1 to 5 of 200 entries

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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 NPC97202 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	172
0.1-0.2	1569
0.2-0.3	3976
0.3-0.4	2277
0.4-0.5	666
0.5-0.6	168
0.6-0.7	149
0.7-0.8	117
0.8-0.85	46
0.85-0.9	10
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8725	High Similarity	NPD5211	Phase 2
0.87	High Similarity	NPD4755	Approved
0.8558	High Similarity	NPD5141	Approved
0.8557	High Similarity	NPD5328	Approved
0.8529	High Similarity	NPD5285	Approved

Showing 1 to 5 of 200 entries

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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