NPASS Compound

Structure

CID102810 OpenBabel06191715452D 46 51 0 0 1 0 0 0 0 0999 V2000 3.6982 -2.5082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9282 -1.7980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2690 -2.4600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1513 -2.4600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0820 -0.2632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1614 -1.5306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6658 -1.3809 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2882 -0.3778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1082 -0.3778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6982 -1.0879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4412 -1.2300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1513 -0.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3212 -0.1813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3026 1.3294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6982 0.3324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8782 0.9971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9172 -0.3600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8198 1.3337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2647 0.3324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1082 -1.7980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4412 -2.0500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6780 -0.4419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8198 0.7522 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7269 0.9971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1513 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5756 0.9971 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.5360 -0.1223 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.5756 0.9971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1513 1.3294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.3294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7269 0.3324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5756 0.3324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7417 0.2273 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.6307 -0.8811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1387 -0.8289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8782 0.3324 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.5246 -0.1574 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.5756 0.3324 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.1513 2.1494 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.1494 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4339 0.4187 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9875 -1.1416 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2267 -1.0598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3026 -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 -1.0574 -0.8289 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 20 1 0 0 0 0 2 20 1 0 0 0 0 3 21 1 0 0 0 0 4 21 1 0 0 0 0 5 22 1 0 0 0 0 6 35 1 0 0 0 0 7 35 1 0 0 0 0 8 36 1 0 0 0 0 9 10 1 0 0 0 0 9 15 1 0 0 0 0 10 20 2 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 17 1 0 0 0 0 13 22 2 0 0 0 0 14 16 2 0 0 0 0 14 24 1 0 0 0 0 15 36 1 0 0 0 0 16 36 1 0 0 0 0 17 37 1 0 0 0 0 18 23 1 0 0 0 0 18 26 1 0 0 0 0 19 23 1 0 0 0 0 19 27 1 0 0 0 0 22 34 1 0 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 26 38 1 0 0 0 0 27 35 1 0 0 0 0 27 38 1 0 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 39 1 0 0 0 0 30 40 2 0 0 0 0 31 44 1 0 0 0 0 32 45 1 0 0 0 0 33 37 1 0 0 0 0 33 41 1 0 0 0 0 34 42 2 0 0 0 0 34 43 1 0 0 0 0 35 46 1 0 0 0 0 36 44 1 0 0 0 0 37 38 1 0 0 0 0 37 46 1 0 0 0 0 38 45 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	632.33
Volume:	661.059
LogP:	7.55
LogD:	4.698
LogS:	-2.996
# Rotatable Bonds:	8
TPSA:	122.52
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	7
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.263
Synthetic Accessibility Score:	7.174
Fsp3:	0.579
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:	-4.982
MDCK Permeability:	1.6860392861417495e-05
Pgp-inhibitor:	0.349
Pgp-substrate:	0.154
Human Intestinal Absorption (HIA):	0.532
20% Bioavailability (F20%):	0.016
30% Bioavailability (F30%):	0.656

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.3
Plasma Protein Binding (PPB):	87.09734344482422%
Volume Distribution (VD):	1.291
Pgp-substrate:	6.732642650604248%

ADMET: Metabolism

CYP1A2-inhibitor:	0.028
CYP1A2-substrate:	0.136
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.432
CYP2C9-inhibitor:	0.142
CYP2C9-substrate:	0.379
CYP2D6-inhibitor:	0.298
CYP2D6-substrate:	0.085
CYP3A4-inhibitor:	0.535
CYP3A4-substrate:	0.273

ADMET: Excretion

Clearance (CL):	1.899
Half-life (T1/2):	0.01

ADMET: Toxicity

hERG Blockers:	0.084
Human Hepatotoxicity (H-HT):	0.97
Drug-inuced Liver Injury (DILI):	0.93
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.975
Maximum Recommended Daily Dose:	0.9
Skin Sensitization:	0.044
Carcinogencity:	0.687
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC102810

Natural Product ID:	NPC102810
*Common Name:**	Tetrahydrogambogic Acid
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CXFIQFGADOTDPF-XKZIYDEJSA-N
Standard InCHI:	InChI=1S/C38H48O8/c1-20(2)10-9-15-36(8)16-14-24-29(39)28-30(40)26-18-23-19-27-35(6,7)46-37(33(23)41,17-13-22(5)34(42)43)38(26,27)45-32(28)25(31(24)44-36)12-11-21(3)4/h10-11,13-14,16,23,26-27,33,39,41H,9,12,15,17-19H2,1-8H3,(H,42,43)/b22-13-
SMILES:	CC(=CCc1c2OC34C(C(=O)c2c(c2c1OC(C)(CCC=C(C)C)C=C2)O)CC1CC3C(OC4(C/C=C(C(=O)O)/C)C1O)(C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1605700
PubChem CID:	9917275
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

Show entries

Search:

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]

Showing 1 to 7 of 7 entries

Previous1Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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	18

Activity Type	# Activity
Individual Protein	14
Others	4

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT149	Individual Protein	Endoplasmic reticulum-associated amyloid beta-peptide-binding protein	Homo sapiens	Potency	=	31622.8	nM	PMID[570125]
NPT48	Individual Protein	Lysine-specific demethylase 4D-like	Homo sapiens	Potency	=	39810.7	nM	PMID[570125]
NPT51	Individual Protein	Microtubule-associated protein tau	Homo sapiens	Potency	=	35481.3	nM	PMID[570125]
NPT442	Individual Protein	Ferritin light chain	Equus caballus	Potency	=	39810.7	nM	PMID[570125]
NPT45	Individual Protein	Ubiquitin carboxyl-terminal hydrolase 2	Homo sapiens	Potency	=	15848.9	nM	PMID[570125]
NPT282	Individual Protein	MAP kinase ERK2	Homo sapiens	Potency	=	39810.7	nM	PMID[570125]
NPT539	Individual Protein	Cellular tumor antigen p53	Homo sapiens	Potency	=	31622.8	nM	PMID[570125]
NPT539	Individual Protein	Cellular tumor antigen p53	Homo sapiens	Potency	=	19952.6	nM	PMID[570125]
NPT443	Individual Protein	Histone acetyltransferase GCN5	Homo sapiens	Potency	n.a.	22387.2	nM	PMID[570125]
NPT198	Individual Protein	Vitamin D receptor	Homo sapiens	Potency	n.a.	50118.7	nM	PMID[570125]

Showing 1 to 10 of 18 entries

Previous1 2Next

☑ 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 NPC102810 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	382
0.1-0.2	1404
0.2-0.3	2992
0.3-0.4	5550
0.4-0.5	10014
0.5-0.6	8110
0.6-0.7	5874
0.7-0.8	7622
0.8-0.85	677
0.85-0.9	61
0.9-0.95	9
0.95-1	2

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
0.9515	High Similarity	NPC476199
0.9515	High Similarity	NPC476210
0.9448	High Similarity	NPC476196
0.9333	High Similarity	NPC476311
0.9268	High Similarity	NPC476146

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC102810 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	331
0.1-0.2	884
0.2-0.3	1861
0.3-0.4	2574
0.4-0.5	2060
0.5-0.6	970
0.6-0.7	315
0.7-0.8	149
0.8-0.85	6
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8606	High Similarity	NPD7075	Discontinued
0.8537	High Similarity	NPD7819	Suspended
0.8485	Intermediate Similarity	NPD8443	Clinical (unspecified phase)
0.8466	Intermediate Similarity	NPD4380	Phase 2
0.8424	Intermediate Similarity	NPD7096	Clinical (unspecified phase)

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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