NPASS Compound

Structure

NPC187263 OpenBabel06302216182D 33 35 0 0 1 0 0 0 0 0999 V2000 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 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 0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 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 33 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 29 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 32 1 0 0 0 0 7 8 1 0 0 0 0 7 20 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 16 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 1 0 0 0 14 16 1 0 0 0 0 16 17 1 1 0 0 0 17 18 1 1 0 0 0 17 19 1 0 0 0 0 20 28 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 21 29 1 0 0 0 0 22 23 1 0 0 0 0 22 24 2 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	454.24
Volume:	481.528
LogP:	6.112
LogD:	4.055
LogS:	-4.321
# Rotatable Bonds:	6
TPSA:	96.97
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.355
Synthetic Accessibility Score:	4.356
Fsp3:	0.481
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:	-4.861
MDCK Permeability:	1.4692644072056282e-05
Pgp-inhibitor:	0.972
Pgp-substrate:	0.863
Human Intestinal Absorption (HIA):	0.044
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.035
Plasma Protein Binding (PPB):	94.78710174560547%
Volume Distribution (VD):	1.179
Pgp-substrate:	5.799621105194092%

ADMET: Metabolism

CYP1A2-inhibitor:	0.333
CYP1A2-substrate:	0.942
CYP2C19-inhibitor:	0.633
CYP2C19-substrate:	0.563
CYP2C9-inhibitor:	0.887
CYP2C9-substrate:	0.809
CYP2D6-inhibitor:	0.128
CYP2D6-substrate:	0.219
CYP3A4-inhibitor:	0.403
CYP3A4-substrate:	0.235

ADMET: Excretion

Clearance (CL):	5.065
Half-life (T1/2):	0.102

ADMET: Toxicity

hERG Blockers:	0.011
Human Hepatotoxicity (H-HT):	0.948
Drug-inuced Liver Injury (DILI):	0.881
AMES Toxicity:	0.058
Rat Oral Acute Toxicity:	0.716
Maximum Recommended Daily Dose:	0.215
Skin Sensitization:	0.598
Carcinogencity:	0.454
Eye Corrosion:	0.003
Eye Irritation:	0.017
Respiratory Toxicity:	0.897

Download Data

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

Natural Product: NPC187263

Natural Product ID:	NPC187263
*Common Name:**	DMYAAHDGSITLHJ-LIVBEALHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DMYAAHDGSITLHJ-LIVBEALHSA-N
Standard InCHI:	InChI=1S/C27H34O6/c1-13(2)11-12-19-24(30)22(23(29)18-10-8-9-14(3)20(18)17(6)28)26-21(25(19)32-7)15(4)16(5)27(31)33-26/h10-11,14,17,20,28,30H,8-9,12H2,1-7H3/t14-,17+,20+/m1/s1
SMILES:	CC(=CCc1c(c(C(=O)C2=CCC[C@@H](C)[C@H]2[C@H](C)O)c2c(c(C)c(C)c(=O)o2)c1OC)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0002908] Hydroxycoumarins [CHEMONTID:0002909] 7-hydroxycoumarins

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0040-4039(00)90246-6]
NPO6617	Chirita eburnea	Species	Gesneriaceae	Eukaryota	whole plant	Guangxi Province, China	2002-AUG	PMID[15921435]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5523	Picria felterrae	Species	Linderniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6202	Aglaomorpha coronans	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6617	Chirita eburnea	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1917	Prosopis nigra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4723	Phanerochaete velutina	Species	Phanerochaetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5523	Picria felterrae	Species	Linderniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5660	Scleropyrum maingayi	Species	Cervantesiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO64	Lysidice brevicalyx	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6202	Aglaomorpha coronans	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3806	Garcinia morella	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC187263 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	351
0.1-0.2	1430
0.2-0.3	3501
0.3-0.4	7203
0.4-0.5	11735
0.5-0.6	4823
0.6-0.7	5923
0.7-0.8	5294
0.8-0.85	1810
0.85-0.9	538
0.9-0.95	87
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID

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 NPC187263 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	319
0.1-0.2	979
0.2-0.3	1876
0.3-0.4	2543
0.4-0.5	2017
0.5-0.6	950
0.6-0.7	316
0.7-0.8	110
0.8-0.85	32
0.85-0.9	6
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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