NPASS Compound

Structure

NPC262649 OpenBabel06302215552D 44 48 0 0 1 0 0 0 0 0999 V2000 2.7596 -5.2092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7415 -4.6424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7415 -3.5086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7233 -2.9417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7233 -1.8080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7415 -1.2411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7596 -1.8080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7778 -1.2411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7778 -0.1074 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7959 0.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7959 1.3786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.8381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7959 1.3786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5918 1.8381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5918 2.9718 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3877 1.3786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7254 1.8441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7254 1.0400 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2259 0.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8508 -0.1691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7837 -1.1461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3588 -2.1391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5296 -1.9273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0539 -1.1461 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6999 -0.2176 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2426 -0.4978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7883 -0.2233 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2988 -0.5586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8445 -0.2841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2637 -1.1684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0000 0.3143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9929 0.5889 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3877 0.4595 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5918 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7959 0.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.1338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9819 -1.7006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9819 -2.8344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9637 -3.4013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.9718 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7415 -0.1074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7233 -5.2092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 44 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 43 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 36 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 12 42 1 0 0 0 0 13 35 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 17 2 0 0 0 0 18 17 1 6 0 0 0 18 19 1 0 0 0 0 18 31 1 0 0 0 0 20 19 1 1 0 0 0 20 21 1 0 0 0 0 20 33 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 21 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 6 0 0 0 25 31 1 0 0 0 0 25 33 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 31 32 2 0 0 0 0 33 16 1 6 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 39 40 1 0 0 0 0 39 41 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	600.35
Volume:	649.398
LogP:	9.292
LogD:	5.658
LogS:	-5.076
# Rotatable Bonds:	10
TPSA:	82.06
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.272
Synthetic Accessibility Score:	6.336
Fsp3:	0.526
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:	-4.793
MDCK Permeability:	1.9496837921906263e-05
Pgp-inhibitor:	0.942
Pgp-substrate:	0.715
Human Intestinal Absorption (HIA):	0.186
20% Bioavailability (F20%):	0.976
30% Bioavailability (F30%):	0.806

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.025
Plasma Protein Binding (PPB):	90.60790252685547%
Volume Distribution (VD):	2.668
Pgp-substrate:	10.274953842163086%

ADMET: Metabolism

CYP1A2-inhibitor:	0.117
CYP1A2-substrate:	0.146
CYP2C19-inhibitor:	0.777
CYP2C19-substrate:	0.388
CYP2C9-inhibitor:	0.933
CYP2C9-substrate:	0.341
CYP2D6-inhibitor:	0.641
CYP2D6-substrate:	0.095
CYP3A4-inhibitor:	0.795
CYP3A4-substrate:	0.656

ADMET: Excretion

Clearance (CL):	13.633
Half-life (T1/2):	0.008

ADMET: Toxicity

hERG Blockers:	0.912
Human Hepatotoxicity (H-HT):	0.982
Drug-inuced Liver Injury (DILI):	0.46
AMES Toxicity:	0.015
Rat Oral Acute Toxicity:	0.945
Maximum Recommended Daily Dose:	0.945
Skin Sensitization:	0.27
Carcinogencity:	0.555
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.97

Download Data

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

Natural Product: NPC262649

Natural Product ID:	NPC262649
*Common Name:**	CYSGOBSZQASJBE-WOQRFNKWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CYSGOBSZQASJBE-WOQRFNKWSA-N
Standard InCHI:	InChI=1S/C38H48O6/c1-22(2)11-10-12-25(7)16-18-42-30-21-29(39)32-33(40)28-19-26-20-31-36(8,9)44-37(35(26)41,17-15-24(5)6)38(28,31)43-34(32)27(30)14-13-23(3)4/h11,13,15-16,19,21,26,31,39H,10,12,14,17-18,20H2,1-9H3/b25-16+/t26-,31+,37+,38-/m1/s1
SMILES:	CC(=CCC/C(=C/COc1cc(c2C(=O)C3=C[C@@H]4C[C@H]5C(C)(C)O[C@@](CC=C(C)C)(C4=O)[C@@]35Oc2c1CC=C(C)C)O)/C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	25208760
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

*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]
NPO17342	Microcosmus vulgaris	Species	Pyuridae	Eukaryota	n.a.	n.a.	n.a.	PMID[10785429]
NPO28098	Rhizomnium pseudopunctatum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19508	Toxicodendron radicans	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15765	Vernonanthura discolor	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11950	Ruscus hypoglossum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13310	Garcinia hanburyi	Species	Clusiaceae	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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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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 NPC262649 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	421
0.1-0.2	1608
0.2-0.3	3127
0.3-0.4	7278
0.4-0.5	10749
0.5-0.6	5466
0.6-0.7	5892
0.7-0.8	6843
0.8-0.85	1198
0.85-0.9	59
0.9-0.95	31
0.95-1	25

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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 NPC262649 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	366
0.1-0.2	922
0.2-0.3	1787
0.3-0.4	2637
0.4-0.5	1977
0.5-0.6	964
0.6-0.7	344
0.7-0.8	145
0.8-0.85	8
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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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