NPASS Compound

Structure

NPC476146 OpenBabel07101719522D 48 53 0 0 1 0 0 0 0 0999 V2000 0.4568 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1888 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3722 -3.8147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6419 -1.7342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7759 -1.2342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8246 -0.0761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5155 0.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1419 0.1319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1419 0.1319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6419 -0.7342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3228 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4568 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3195 -2.3646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9135 0.5274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1419 0.1319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6419 -0.7342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1419 0.3956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4823 -1.8177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0224 0.4771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3202 0.7842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3228 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2644 -3.3631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1774 0.2637 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6851 0.3956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4568 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2284 0.3956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0374 0.7196 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2284 0.3956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4568 0.5274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.5274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6851 0.1319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2284 0.1319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0808 -0.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1016 -3.9100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6419 -0.7342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8464 0.1319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1419 0.1319 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.5374 -0.8192 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2284 0.1319 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4568 1.5274 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.5274 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9153 -1.0008 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0466 -4.9085 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9939 -3.4585 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6419 -0.7342 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9135 -0.0000 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 -1.5374 -0.8192 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 21 1 0 0 0 0 2 21 1 0 0 0 0 3 22 1 0 0 0 0 4 35 1 0 0 0 0 5 35 1 0 0 0 0 6 36 1 0 0 0 0 7 36 1 0 0 0 0 8 37 1 0 0 0 0 9 10 1 0 0 0 0 9 15 2 0 0 0 0 10 16 1 0 0 0 0 11 12 1 0 0 0 0 11 21 2 0 0 0 0 12 25 1 0 0 0 0 13 18 1 0 0 0 0 13 22 2 0 0 0 0 14 17 2 0 0 0 0 14 24 1 0 0 0 0 15 35 1 0 0 0 0 16 37 1 0 0 0 0 17 37 1 0 0 0 0 18 38 1 0 0 0 0 19 26 2 0 0 0 0 20 23 1 0 0 0 0 20 27 1 0 0 0 0 22 34 1 0 0 0 0 23 19 1 1 0 0 0 23 33 1 0 0 0 0 24 29 2 0 0 0 0 24 31 1 0 0 0 0 25 31 2 0 0 0 0 25 32 1 0 0 0 0 26 30 1 0 0 0 0 27 36 1 0 0 0 0 27 39 1 1 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 28 32 2 0 0 0 0 29 40 1 0 0 0 0 30 41 2 0 0 0 0 31 46 1 0 0 0 0 32 47 1 0 0 0 0 33 38 1 0 0 0 0 33 42 2 0 0 0 0 34 43 2 0 0 0 0 34 44 1 0 0 0 0 35 45 1 0 0 0 0 36 48 1 0 0 0 0 37 46 1 0 0 0 0 38 39 1 1 0 0 0 38 48 1 0 0 0 0 39 26 1 6 0 0 0 39 47 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	658.31
Volume:	681.872
LogP:	6.833
LogD:	3.091
LogS:	-3.051
# Rotatable Bonds:	9
TPSA:	139.59
# H-Bond Aceptor:	9
# H-Bond Donor:	3
# Rings:	7
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.255
Synthetic Accessibility Score:	7.105
Fsp3:	0.513
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:	-4.904
MDCK Permeability:	1.622982381377369e-05
Pgp-inhibitor:	0.779
Pgp-substrate:	0.01
Human Intestinal Absorption (HIA):	0.585
20% Bioavailability (F20%):	0.015
30% Bioavailability (F30%):	0.102

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.389
Plasma Protein Binding (PPB):	99.72093963623047%
Volume Distribution (VD):	1.177
Pgp-substrate:	3.9836134910583496%

ADMET: Metabolism

CYP1A2-inhibitor:	0.036
CYP1A2-substrate:	0.272
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.372
CYP2C9-inhibitor:	0.258
CYP2C9-substrate:	0.268
CYP2D6-inhibitor:	0.197
CYP2D6-substrate:	0.065
CYP3A4-inhibitor:	0.615
CYP3A4-substrate:	0.639

ADMET: Excretion

Clearance (CL):	1.223
Half-life (T1/2):	0.115

ADMET: Toxicity

hERG Blockers:	0.062
Human Hepatotoxicity (H-HT):	0.923
Drug-inuced Liver Injury (DILI):	0.954
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.988
Maximum Recommended Daily Dose:	0.942
Skin Sensitization:	0.144
Carcinogencity:	0.953
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.975

Download Data

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

Natural Product: NPC476146

Natural Product ID:	NPC476146
*Common Name:**	Oxygambogic Acid
IUPAC Name:	n.a.
Synonyms:	Oxygambogic Acid
Standard InCHIKey:	DXSGQRROBDYCSJ-YVMJPLCQSA-N
Standard InCHI:	InChI=1S/C39H46O9/c1-21(2)11-12-25-31-24(14-17-37(8,46-31)16-10-9-15-35(4,5)45)29(40)28-30(41)26-19-23-20-27-36(6,7)48-38(33(23)42,18-13-22(3)34(43)44)39(26,27)47-32(25)28/h9,11,13-15,17,19,23,27,40,45H,10,12,16,18,20H2,1-8H3,(H,43,44)/b15-9+,22-13-/t23-,27+,37?,38+,39-/m1/s1
SMILES:	CC(=CCC1=C2C(=C(C3=C1OC45C6CC(C=C4C3=O)C(=O)C5(OC6(C)C)CC=C(C)C(=O)O)O)C=CC(O2)(C)CCC=CC(C)(C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL540663
PubChem CID:	45267154
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones [CHEMONTID:0003521] Pyranoxanthones

*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
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21486005]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	resin	n.a.	n.a.	PMID[19072548]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	latex	n.a.	PMID[17117343]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[17117343]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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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	1

Activity Type	# Activity
Cell Line	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	1910.0	nM	PMID[575606]

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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 NPC476146 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	399
0.1-0.2	1602
0.2-0.3	3207
0.3-0.4	7097
0.4-0.5	10770
0.5-0.6	6254
0.6-0.7	5926
0.7-0.8	7094
0.8-0.85	271
0.85-0.9	31
0.9-0.95	27
0.95-1	19

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC40089
1.0	High Similarity	NPC158329
0.9874	High Similarity	NPC55422
0.9874	High Similarity	NPC75141
0.9874	High Similarity	NPC47634

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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 NPC476146 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	346
0.1-0.2	963
0.2-0.3	1880
0.3-0.4	2695
0.4-0.5	1964
0.5-0.6	884
0.6-0.7	283
0.7-0.8	132
0.8-0.85	3
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
0.8494	Intermediate Similarity	NPD7075	Discontinued
0.8313	Intermediate Similarity	NPD7819	Suspended
0.8313	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.8263	Intermediate Similarity	NPD8443	Clinical (unspecified phase)
0.8198	Intermediate Similarity	NPD7852	Clinical (unspecified phase)

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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