NPASS Compound

Structure

NPC102067 OpenBabel06302215562D 36 43 0 0 0 0 0 0 0 0999 V2000 -2.5390 -1.4659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5390 -0.4886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6927 -0.0000 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 -0.8463 -1.4659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6927 -1.9545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.9545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8463 -1.4659 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 1.7758 -0.1866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1733 0.7061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1452 0.8083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7196 0.0177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3221 -0.8751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3502 -0.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7758 -1.7679 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.9318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8463 -3.4205 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6927 -3.9091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6927 -4.8864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8463 -5.3750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8463 -6.3523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6927 -6.8409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5390 -6.3523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5390 -5.3750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3854 -4.8864 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.3854 -3.9091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1116 -3.2552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0835 -3.3573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6580 -2.5667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2605 -1.6739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2886 -1.5718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7141 -2.3624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7422 -2.4645 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5390 -3.4205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 17 2 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 7 2 0 0 0 0 7 8 1 0 0 0 0 7 18 1 0 0 0 0 8 16 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 9 17 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 36 2 0 0 0 0 20 21 1 0 0 0 0 21 26 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 28 36 1 0 0 0 0 28 29 1 0 0 0 0 29 34 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	462.15
Volume:	484.238
LogP:	6.395
LogD:	4.697
LogS:	-8.603
# Rotatable Bonds:	2
TPSA:	74.43
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	8
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.265
Synthetic Accessibility Score:	2.507
Fsp3:	0.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.673
MDCK Permeability:	1.0231339729216415e-05
Pgp-inhibitor:	0.944
Pgp-substrate:	0.734
Human Intestinal Absorption (HIA):	0.158
20% Bioavailability (F20%):	0.989
30% Bioavailability (F30%):	0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.012
Plasma Protein Binding (PPB):	101.02216339111328%
Volume Distribution (VD):	1.108
Pgp-substrate:	1.1119776964187622%

ADMET: Metabolism

CYP1A2-inhibitor:	0.989
CYP1A2-substrate:	0.21
CYP2C19-inhibitor:	0.632
CYP2C19-substrate:	0.061
CYP2C9-inhibitor:	0.371
CYP2C9-substrate:	0.493
CYP2D6-inhibitor:	0.178
CYP2D6-substrate:	0.533
CYP3A4-inhibitor:	0.378
CYP3A4-substrate:	0.171

ADMET: Excretion

Clearance (CL):	2.95
Half-life (T1/2):	0.018

ADMET: Toxicity

hERG Blockers:	0.069
Human Hepatotoxicity (H-HT):	0.951
Drug-inuced Liver Injury (DILI):	0.97
AMES Toxicity:	0.562
Rat Oral Acute Toxicity:	0.135
Maximum Recommended Daily Dose:	0.879
Skin Sensitization:	0.94
Carcinogencity:	0.869
Eye Corrosion:	0.003
Eye Irritation:	0.887
Respiratory Toxicity:	0.369

Download Data

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

Natural Product: NPC102067

Natural Product ID:	NPC102067
*Common Name:**	BOMINIHNGZWSLU-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BOMINIHNGZWSLU-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C31H18N4O/c36-31(25-17-9-1-5-13-21(17)32-27-19-11-3-7-15-23(19)34-29(25)27)26-18-10-2-6-14-22(18)33-28-20-12-4-8-16-24(20)35-30(26)28/h1-16,34-35H
SMILES:	c1ccc2c(c1)c(c1c(c3ccccc3[nH]1)n2)C(=O)c1c2ccccc2nc2c3ccccc3[nH]c12
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10600127
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001253] Quinolines and derivatives [CHEMONTID:0000061] Indoloquinolines

*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
NPO20237	Poecillastra wondoensis	Species	Vulcanellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[14640526]
NPO20237	Poecillastra wondoensis	Species	Vulcanellidae	Eukaryota	n.a.	depth of 25 m off the shore of Keomun Island, Korea	2004-AUG	PMID[18407691]
NPO20912	Wisteria brachybotrys	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2853205]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[32998509]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24783	Erysimum diffusum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24783	Erysimum diffusum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24783	Erysimum diffusum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20912	Wisteria brachybotrys	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20237	Poecillastra wondoensis	Species	Vulcanellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17131	Yucca periculosa	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20299	Strongylophora durissima	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO18755	Fumaria judaica	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21890	Epidendrum moseni	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO20169	Alseodaphne perakensis	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20989	Calea integrifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11155	Ambrosia maritima	Species	Asteraceae	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 NPC102067 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	868
0.1-0.2	6159
0.2-0.3	16527
0.3-0.4	14039
0.4-0.5	1768
0.5-0.6	2026
0.6-0.7	1147
0.7-0.8	147
0.8-0.85	13
0.85-0.9	3
0.9-0.95	0
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 NPC102067 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	495
0.1-0.2	674
0.2-0.3	1131
0.3-0.4	2591
0.4-0.5	2145
0.5-0.6	1651
0.6-0.7	447
0.7-0.8	16
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