NPASS Compound

Structure

NPC121636 OpenBabel06302215272D 26 29 0 0 0 0 0 0 0 0999 V2000 1.7392 3.8619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7264 2.8928 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8732 2.4209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0385 2.9151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8029 2.4430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6330 2.9370 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4759 2.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4887 1.4991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6585 1.0051 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8156 1.4771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0128 0.9717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8604 1.4549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7007 0.9494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5426 1.4327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3781 0.9416 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5553 2.3987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4012 2.8718 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6879 -0.0223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8463 -0.4886 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 -0.8481 -0.4744 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5054 -1.3838 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8378 -1.4508 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6669 -1.9392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5137 -0.5161 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2751 0.0721 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 16 1 0 0 0 0 2 3 1 0 0 0 0 3 12 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 10 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 20 1 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 13 18 2 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 19 1 0 0 0 0 18 25 1 0 0 0 0 19 20 2 0 0 0 0 19 23 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	351.11
Volume:	351.47
LogP:	3.016
LogD:	2.634
LogS:	-6.031
# Rotatable Bonds:	3
TPSA:	65.07
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.536
Synthetic Accessibility Score:	2.651
Fsp3:	0.2
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.618
MDCK Permeability:	4.1322004108224064e-05
Pgp-inhibitor:	0.87
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.124
Plasma Protein Binding (PPB):	86.28699493408203%
Volume Distribution (VD):	0.6
Pgp-substrate:	11.314472198486328%

ADMET: Metabolism

CYP1A2-inhibitor:	0.831
CYP1A2-substrate:	0.971
CYP2C19-inhibitor:	0.759
CYP2C19-substrate:	0.907
CYP2C9-inhibitor:	0.73
CYP2C9-substrate:	0.889
CYP2D6-inhibitor:	0.323
CYP2D6-substrate:	0.509
CYP3A4-inhibitor:	0.537
CYP3A4-substrate:	0.565

ADMET: Excretion

Clearance (CL):	1.685
Half-life (T1/2):	0.165

ADMET: Toxicity

hERG Blockers:	0.039
Human Hepatotoxicity (H-HT):	0.17
Drug-inuced Liver Injury (DILI):	0.934
AMES Toxicity:	0.76
Rat Oral Acute Toxicity:	0.384
Maximum Recommended Daily Dose:	0.095
Skin Sensitization:	0.468
Carcinogencity:	0.278
Eye Corrosion:	0.006
Eye Irritation:	0.692
Respiratory Toxicity:	0.179

Download Data

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

Natural Product: NPC121636

Natural Product ID:	NPC121636
*Common Name:**	WCRCWNWYSVULNX-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WCRCWNWYSVULNX-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C20H17NO5/c1-21-12-9-10-7-5-6-8-11(10)13-14(12)15(16(22)20(21)23)18(25-3)19(26-4)17(13)24-2/h5-9H,1-4H3
SMILES:	CN1c2cc3ccccc3c3c2c(C(=O)C1=O)c(c(c3OC)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11210309
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0000381] Aporphines [CHEMONTID:0003326] 4,5-dioxoaporphines

*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
NPO5928	Streptomyces nashvillensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1490884]
NPO7929	Curcuma zedoaria	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9868158]
NPO7929	Curcuma zedoaria	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11088	Ganoderma capense	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7929	Curcuma zedoaria	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11088	Ganoderma capense	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7929	Curcuma zedoaria	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7929	Curcuma zedoaria	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11715	Polygonum aubertii	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7929	Curcuma zedoaria	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3584	Oyedaea buphthalmoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12667	Goniodoma pseudogoniaulax	Species	Coleophoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11088	Ganoderma capense	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11010	Melampyrum elatius	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9030	Couroupita guianensis	Species	Lecythidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO868	Cephalaria gigantea	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5928	Streptomyces nashvillensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2400	Streptomyces mediolani	Species	Streptomycetaceae	Bacteria	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 NPC121636 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	514
0.1-0.2	2630
0.2-0.3	10107
0.3-0.4	7194
0.4-0.5	7464
0.5-0.6	10241
0.6-0.7	4339
0.7-0.8	199
0.8-0.85	3
0.85-0.9	4
0.9-0.95	2
0.95-1	0

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 NPC121636 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	312
0.1-0.2	825
0.2-0.3	1047
0.3-0.4	1898
0.4-0.5	2967
0.5-0.6	1652
0.6-0.7	431
0.7-0.8	18
0.8-0.85	0
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