NPASS Compound

Structure

NPC27951 OpenBabel06302215192D 22 24 0 0 0 0 0 0 0 0999 V2000 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 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 0.8660 0.5000 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 2.0000 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 1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 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 -0.8660 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 -2.5981 0.5000 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 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 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 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 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 21 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 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 21 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 19 1 0 0 0 0 15 16 1 0 0 0 0 15 18 1 0 0 0 0 16 17 1 0 0 0 0 19 20 1 0 0 0 0 21 22 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	318.03
Volume:	297.693
LogP:	4.597
LogD:	2.746
LogS:	-5.636
# Rotatable Bonds:	1
TPSA:	83.83
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.72
Synthetic Accessibility Score:	2.503
Fsp3:	0.125
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.021
MDCK Permeability:	1.5673727830289863e-05
Pgp-inhibitor:	0.247
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.061
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.973

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.027
Plasma Protein Binding (PPB):	100.80636596679688%
Volume Distribution (VD):	0.343
Pgp-substrate:	0.8837459683418274%

ADMET: Metabolism

CYP1A2-inhibitor:	0.916
CYP1A2-substrate:	0.893
CYP2C19-inhibitor:	0.219
CYP2C19-substrate:	0.075
CYP2C9-inhibitor:	0.715
CYP2C9-substrate:	0.383
CYP2D6-inhibitor:	0.176
CYP2D6-substrate:	0.192
CYP3A4-inhibitor:	0.313
CYP3A4-substrate:	0.163

ADMET: Excretion

Clearance (CL):	6.714
Half-life (T1/2):	0.153

ADMET: Toxicity

hERG Blockers:	0.021
Human Hepatotoxicity (H-HT):	0.093
Drug-inuced Liver Injury (DILI):	0.94
AMES Toxicity:	0.81
Rat Oral Acute Toxicity:	0.23
Maximum Recommended Daily Dose:	0.921
Skin Sensitization:	0.204
Carcinogencity:	0.677
Eye Corrosion:	0.003
Eye Irritation:	0.938
Respiratory Toxicity:	0.162

Download Data

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

Natural Product: NPC27951

Natural Product ID:	NPC27951
*Common Name:**	RTBAOFRCWWQFHB-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RTBAOFRCWWQFHB-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C16H11ClO5/c1-6-3-7-11(9(18)4-6)15(20)12-8(14(7)19)5-10(22-2)13(17)16(12)21/h3-5,18,21H,1-2H3
SMILES:	Cc1cc2c(c(c1)O)C(=O)c1c(cc(c(c1O)Cl)OC)C2=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15559331
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones

*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
NPO16100	Eremostachys glabra	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15387666]
NPO512	Aka coralliphaga	Species	Niphatidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16408905]
NPO15650	Picea neoveitchii	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22901896]
NPO10913	Scleroderma citrinum	Species	Sclerodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10913	Scleroderma citrinum	Species	Sclerodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5144	Berberis japonica	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10976	Nicandra physalodes	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15650	Picea neoveitchii	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10976	Nicandra physalodes	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10913	Scleroderma citrinum	Species	Sclerodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16100	Eremostachys glabra	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO84	Isoberlinia angolensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24501	Asteriscus graveolens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5144	Berberis japonica	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20964	Picradeniopsis oppositifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO512	Aka coralliphaga	Species	Niphatidae	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 NPC27951 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	476
0.1-0.2	2213
0.2-0.3	5522
0.3-0.4	12660
0.4-0.5	5026
0.5-0.6	5782
0.6-0.7	5949
0.7-0.8	4735
0.8-0.85	248
0.85-0.9	62
0.9-0.95	21
0.95-1	3

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 NPC27951 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	449
0.1-0.2	1068
0.2-0.3	1828
0.3-0.4	2872
0.4-0.5	1737
0.5-0.6	867
0.6-0.7	251
0.7-0.8	77
0.8-0.85	1
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