NPASS Compound

Structure

NPC176187 OpenBabel06302216022D 40 45 0 0 1 0 0 0 0 0999 V2000 5.0832 -4.8913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0832 -3.9130 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2360 -3.4239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2360 -2.4457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0832 -1.9565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9304 -2.4457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9304 -3.4239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7776 -1.9565 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0832 -0.9783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9304 -0.4891 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2360 -0.4891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2360 0.4891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3888 0.9783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5416 0.4891 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5416 -0.4891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3888 -0.9783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3888 -1.9565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5416 -2.4457 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8472 -1.4674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8472 -1.4674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8472 -2.4457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.9348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8472 -2.4457 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6944 -2.9348 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6944 -2.9348 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6944 -0.9783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5416 -1.4674 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6944 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8472 0.4891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8472 1.4674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6944 1.9565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6944 2.9348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5416 1.4674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5416 0.4891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3888 -0.0000 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 0.8472 0.4891 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6944 0.9783 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0832 0.9783 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 7 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 17 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 9 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 16 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 12 40 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 39 1 1 0 0 0 15 16 2 0 0 0 0 15 19 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 19 24 1 0 0 0 0 19 20 2 0 0 0 0 20 37 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 27 1 0 0 0 0 22 23 1 0 0 0 0 22 26 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 6 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 29 35 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 37 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 32 34 2 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 37 38 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	542.12
Volume:	527.089
LogP:	6.943
LogD:	2.469
LogS:	-4.48
# Rotatable Bonds:	1
TPSA:	202.3
# H-Bond Aceptor:	10
# H-Bond Donor:	10
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.091
Synthetic Accessibility Score:	3.152
Fsp3:	0.067
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.361
MDCK Permeability:	4.147500021645101e-06
Pgp-inhibitor:	0.032
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.997
20% Bioavailability (F20%):	0.179
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0
Plasma Protein Binding (PPB):	92.72947692871094%
Volume Distribution (VD):	0.216
Pgp-substrate:	16.980934143066406%

ADMET: Metabolism

CYP1A2-inhibitor:	0.869
CYP1A2-substrate:	0.202
CYP2C19-inhibitor:	0.036
CYP2C19-substrate:	0.035
CYP2C9-inhibitor:	0.526
CYP2C9-substrate:	0.323
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.184
CYP3A4-inhibitor:	0.007
CYP3A4-substrate:	0.013

ADMET: Excretion

Clearance (CL):	5.958
Half-life (T1/2):	0.587

ADMET: Toxicity

hERG Blockers:	0.016
Human Hepatotoxicity (H-HT):	0.095
Drug-inuced Liver Injury (DILI):	0.987
AMES Toxicity:	0.128
Rat Oral Acute Toxicity:	0.005
Maximum Recommended Daily Dose:	0.956
Skin Sensitization:	0.956
Carcinogencity:	0.024
Eye Corrosion:	0.004
Eye Irritation:	0.937
Respiratory Toxicity:	0.019

Download Data

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

Natural Product: NPC176187

Natural Product ID:	NPC176187
*Common Name:**	SMIDBNIORCUJSX-IYBDPMFKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SMIDBNIORCUJSX-IYBDPMFKSA-N
Standard InCHI:	InChI=1S/C30H22O10/c1-9-3-11-19(13(31)5-9)29(39)23-17(35)7-15(33)21(25(23)27(11)37)22-16(34)8-18(36)24-26(22)28(38)12-4-10(2)6-14(32)20(12)30(24)40/h3-6,15-16,31-36H,7-8H2,1-2H3/t15-,16+
SMILES:	Cc1cc2c(c(c1)O)C(=O)C1=C(C[C@@H](C(=C1C2=O)C1=C2C(=C(C[C@H]1O)O)C(=O)c1c(cc(C)cc1O)C2=O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones [CHEMONTID:0001598] Hydroxyanthraquinones

*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
NPO8046	Muntingia calabura	Species	Muntingiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[2045815]
NPO8046	Muntingia calabura	Species	Muntingiaceae	Eukaryota	n.a.	root	n.a.	PMID[2045815]
NPO8046	Muntingia calabura	Species	Muntingiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8046	Muntingia calabura	Species	Muntingiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4263	Andrographis laxiflora	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5252	Micromonospora megalomicea	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5787	Passiflora sexflora	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO72	Aspergillus silvaticus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10058	Salvia aurea	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8046	Muntingia calabura	Species	Muntingiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7899	Bridelia stipularis	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4102	Cephalotaxus griffithii	Species	Taxaceae	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 NPC176187 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	328
0.1-0.2	1354
0.2-0.3	2874
0.3-0.4	7923
0.4-0.5	11859
0.5-0.6	5803
0.6-0.7	9180
0.7-0.8	3039
0.8-0.85	267
0.85-0.9	65
0.9-0.95	4
0.95-1	1

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 NPC176187 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	296
0.1-0.2	920
0.2-0.3	1462
0.3-0.4	2648
0.4-0.5	2276
0.5-0.6	1101
0.6-0.7	380
0.7-0.8	61
0.8-0.85	6
0.85-0.9	0
0.9-0.95	0
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