NPASS Compound

Structure

NPC474464 OpenBabel07101719522D 33 38 0 0 1 0 0 0 0 0999 V2000 -2.4271 2.7634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2601 2.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0880 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8966 1.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3559 -2.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8200 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9540 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3559 0.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7226 1.1810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9540 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5388 -1.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7045 2.5823 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6180 2.1756 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9511 1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0880 -2.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8200 -2.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2219 -0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3559 -1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9135 0.5933 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0880 -1.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4899 0.1910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4899 -0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5388 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.6861 -2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0181 -0.4013 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8966 -1.7226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1266 1.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1045 1.9945 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 2 16 1 0 0 0 0 4 24 1 0 0 0 0 5 6 1 0 0 0 0 5 17 2 0 0 0 0 6 20 1 0 0 0 0 7 9 1 0 0 0 0 7 18 1 0 0 0 0 8 10 1 0 0 0 0 8 19 1 0 0 0 0 9 23 1 0 0 0 0 10 24 1 0 0 0 0 11 15 1 0 0 0 0 11 21 1 0 0 0 0 12 17 1 0 0 0 0 12 18 1 0 0 0 0 13 22 1 0 0 0 0 13 25 1 0 0 0 0 14 15 1 0 0 0 0 14 32 1 0 0 0 0 15 1 1 1 0 0 0 16 26 1 1 0 0 0 16 27 1 0 0 0 0 17 23 1 0 0 0 0 18 28 1 6 0 0 0 19 20 1 0 0 0 0 19 23 1 6 0 0 0 20 25 1 1 0 0 0 21 27 1 1 0 0 0 21 29 1 0 0 0 0 22 26 1 6 0 0 0 22 33 1 0 0 0 0 23 3 1 6 0 0 0 24 25 1 6 0 0 0 25 30 1 1 0 0 0 26 24 1 6 0 0 0 26 31 1 0 0 0 0 27 32 1 1 0 0 0 27 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	462.3
Volume:	474.314
LogP:	3.186
LogD:	2.351
LogS:	-4.126
# Rotatable Bonds:	0
TPSA:	99.38
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.413
Synthetic Accessibility Score:	5.944
Fsp3:	0.926
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:	-4.749
MDCK Permeability:	1.3402691365627106e-05
Pgp-inhibitor:	0.496
Pgp-substrate:	0.995
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.57
30% Bioavailability (F30%):	0.026

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.526
Plasma Protein Binding (PPB):	92.43267822265625%
Volume Distribution (VD):	0.858
Pgp-substrate:	4.200662136077881%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.834
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.741
CYP2C9-inhibitor:	0.039
CYP2C9-substrate:	0.024
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.213
CYP3A4-inhibitor:	0.451
CYP3A4-substrate:	0.19

ADMET: Excretion

Clearance (CL):	6.572
Half-life (T1/2):	0.298

ADMET: Toxicity

hERG Blockers:	0.177
Human Hepatotoxicity (H-HT):	0.744
Drug-inuced Liver Injury (DILI):	0.021
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.399
Maximum Recommended Daily Dose:	0.943
Skin Sensitization:	0.688
Carcinogencity:	0.916
Eye Corrosion:	0.006
Eye Irritation:	0.065
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC474464

Natural Product ID:	NPC474464
*Common Name:**	ACGOWVMZBJLEQS-ICCXABGJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ACGOWVMZBJLEQS-ICCXABGJSA-N
Standard InCHI:	InChI=1S/C27H42O6/c1-15-11-21(29)27(32-14-15)16(2)26(31)22(33-27)13-25(30)20-6-5-17-12-18(28)7-9-23(17,3)19(20)8-10-24(25,26)4/h5,15-16,18-22,28-31H,6-14H2,1-4H3/t15-,16+,18+,19+,20-,21+,22+,23+,24+,25-,26-,27+/m1/s1
SMILES:	C[C@H]1CO[C@]2([C@H](C1)O)O[C@@H]1[C@@]([C@@H]2C)(O)[C@@]2([C@](C1)(O)[C@@H]1CC=C3[C@]([C@H]1CC2)(C)CC[C@@H](C3)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL469418
PubChem CID:	11454017
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001295] Hydroxysteroids [CHEMONTID:0003236] 17-hydroxysteroids

*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
NPO27960	Dioscorea polygonoides	Species	Dioscoreaceae	Eukaryota	tubers	n.a.	n.a.	PMID[16038563]
NPO27960	Dioscorea polygonoides	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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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
IC50	2

Activity Type	# Activity
Cell Line	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT924	Cell Line	HSC-2	Homo sapiens	IC50	>	200000.0	nM	PMID[550805]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	200000.0	nM	PMID[550805]

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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 NPC474464 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	250
0.1-0.2	1823
0.2-0.3	6083
0.3-0.4	13961
0.4-0.5	8482
0.5-0.6	5280
0.6-0.7	4656
0.7-0.8	1763
0.8-0.85	265
0.85-0.9	120
0.9-0.95	9
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
0.9897	High Similarity	NPC474015
0.9896	High Similarity	NPC475701
0.96	High Similarity	NPC128133
0.9592	High Similarity	NPC471111
0.9485	High Similarity	NPC474022

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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 NPC474464 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	211
0.1-0.2	1985
0.2-0.3	4340
0.3-0.4	1753
0.4-0.5	432
0.5-0.6	205
0.6-0.7	181
0.7-0.8	43
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8158	Intermediate Similarity	NPD8033	Approved
0.8053	Intermediate Similarity	NPD7327	Approved
0.8053	Intermediate Similarity	NPD7328	Approved
0.7982	Intermediate Similarity	NPD7516	Approved
0.7963	Intermediate Similarity	NPD6412	Phase 2

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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