NPASS Compound

Structure

NPC113849 OpenBabel06302215282D 22 24 0 0 1 0 0 0 0 0999 V2000 -0.7071 -0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6730 -0.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9319 0.5176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9319 0.5176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1907 -0.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1566 -0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8637 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6049 0.9659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6390 1.2247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6390 2.2247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9319 2.9319 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8013 3.9233 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8774 4.3060 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9319 2.9319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2247 2.2247 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2247 1.2247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2588 0.9659 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 0.9659 -0.2588 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7252 3.5406 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8296 -0.2588 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4154 -1.6730 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 18 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 16 1 0 0 0 0 3 4 1 0 0 0 0 4 9 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 6 22 1 0 0 0 0 7 8 2 0 0 0 0 7 21 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 14 1 0 0 0 0 11 20 1 1 0 0 0 12 13 2 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	137.08
Volume:	150.245
LogP:	0.982
LogD:	1.261
LogS:	-0.818
# Rotatable Bonds:	2
TPSA:	35.25
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.625
Synthetic Accessibility Score:	1.715
Fsp3:	0.25
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.403
MDCK Permeability:	7.808706141076982e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.956
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.347
Plasma Protein Binding (PPB):	21.52566146850586%
Volume Distribution (VD):	1.346
Pgp-substrate:	68.49061584472656%

ADMET: Metabolism

CYP1A2-inhibitor:	0.3
CYP1A2-substrate:	0.423
CYP2C19-inhibitor:	0.204
CYP2C19-substrate:	0.837
CYP2C9-inhibitor:	0.037
CYP2C9-substrate:	0.08
CYP2D6-inhibitor:	0.103
CYP2D6-substrate:	0.866
CYP3A4-inhibitor:	0.03
CYP3A4-substrate:	0.343

ADMET: Excretion

Clearance (CL):	6.785
Half-life (T1/2):	0.619

ADMET: Toxicity

hERG Blockers:	0.036
Human Hepatotoxicity (H-HT):	0.082
Drug-inuced Liver Injury (DILI):	0.15
AMES Toxicity:	0.889
Rat Oral Acute Toxicity:	0.566
Maximum Recommended Daily Dose:	0.024
Skin Sensitization:	0.863
Carcinogencity:	0.796
Eye Corrosion:	0.264
Eye Irritation:	0.99
Respiratory Toxicity:	0.299

Download Data

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

Natural Product: NPC113849

Natural Product ID:	NPC113849
*Common Name:**	QNHPMVBTMIUVRU-INIZCTEOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QNHPMVBTMIUVRU-INIZCTEOSA-N
Standard InCHI:	InChI=1S/C16H14O6/c17-7-16(21)6-9-3-13(19)14(20)5-12(9)11-2-1-10(18)4-15(11)22-8-16/h1-5,7,18-21H,6,8H2/t16-/m0/s1
SMILES:	c1cc2-c3cc(c(cc3C[C@](C=O)(COc2cc1O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	13846692
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000254] Ethers [CHEMONTID:0000128] Alkyl aryl ethers

*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
NPO2554	Biancaea sappan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2554	Biancaea sappan	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2554	Biancaea sappan	Species	Fabaceae	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 NPC113849 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	402
0.1-0.2	1696
0.2-0.3	4476
0.3-0.4	11572
0.4-0.5	6398
0.5-0.6	3731
0.6-0.7	5819
0.7-0.8	7403
0.8-0.85	1145
0.85-0.9	53
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 NPC113849 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	378
0.1-0.2	943
0.2-0.3	1829
0.3-0.4	2723
0.4-0.5	1655
0.5-0.6	927
0.6-0.7	572
0.7-0.8	110
0.8-0.85	13
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