NPASS Compound

Structure

NPC137767 OpenBabel06302216002D 23 23 0 0 1 0 0 0 0 0999 V2000 3.9836 -0.3136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5714 0.4954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5659 0.3909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1537 1.1999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7469 2.1135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3347 2.9225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3292 2.8180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9170 3.6270 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 4.1646 1.4090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1701 1.5135 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7634 2.4271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9543 3.0148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8498 2.0203 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3511 3.2361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5823 0.7045 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1810 1.7226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3090 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -1.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 -0.9511 0.0000 C 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 -0.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 2 9 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 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 10 9 1 1 0 0 0 10 11 1 0 0 0 0 10 15 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 11 14 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 18 16 1 6 0 0 0 18 19 1 0 0 0 0 18 22 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	339.2
Volume:	361.866
LogP:	3.711
LogD:	3.678
LogS:	-3.169
# Rotatable Bonds:	9
TPSA:	29.54
# H-Bond Aceptor:	3
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.383
Synthetic Accessibility Score:	4.229
Fsp3:	0.632
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:	-4.347
MDCK Permeability:	2.1358408048399724e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.067
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.882
Plasma Protein Binding (PPB):	48.74437713623047%
Volume Distribution (VD):	1.786
Pgp-substrate:	58.093990325927734%

ADMET: Metabolism

CYP1A2-inhibitor:	0.076
CYP1A2-substrate:	0.461
CYP2C19-inhibitor:	0.487
CYP2C19-substrate:	0.939
CYP2C9-inhibitor:	0.077
CYP2C9-substrate:	0.986
CYP2D6-inhibitor:	0.882
CYP2D6-substrate:	0.927
CYP3A4-inhibitor:	0.693
CYP3A4-substrate:	0.775

ADMET: Excretion

Clearance (CL):	6.541
Half-life (T1/2):	0.502

ADMET: Toxicity

hERG Blockers:	0.469
Human Hepatotoxicity (H-HT):	0.705
Drug-inuced Liver Injury (DILI):	0.427
AMES Toxicity:	0.029
Rat Oral Acute Toxicity:	0.219
Maximum Recommended Daily Dose:	0.875
Skin Sensitization:	0.336
Carcinogencity:	0.501
Eye Corrosion:	0.005
Eye Irritation:	0.015
Respiratory Toxicity:	0.961

Download Data

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

Natural Product: NPC137767

Natural Product ID:	NPC137767
*Common Name:**	ACHIHHQMGVRBRM-PWHIEJPTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ACHIHHQMGVRBRM-PWHIEJPTSA-N
Standard InCHI:	InChI=1S/C19H30ClNO2/c1-15(10-7-6-8-12-20)14-17(19(2,3)4)23-18(22)16-11-9-13-21(16)5/h6-8,12,16-17H,1,9-11,13-14H2,2-5H3/b7-6+,12-8+/t16-,17+/m0/s1
SMILES:	C=C(C/C=C/C=C/Cl)C[C@H](C(C)(C)C)OC(=O)[C@@H]1CCCN1C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids and derivatives [CHEMONTID:0000394] Alpha amino acid esters

*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
NPO11600	Scolopendra subspinipes	Species	Scolopendridae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1021/np960188t]
NPO16759	Polyalthia debilis	Species	Annonaceae	Eukaryota	n.a.	root	n.a.	PMID[12762793]
NPO11600	Scolopendra subspinipes	Species	Scolopendridae	Eukaryota	n.a.	n.a.	n.a.	PMID[16595909]
NPO12302	Hebanthe paniculata	Species	Amaranthaceae	Eukaryota	n.a.	root	n.a.	PMID[19941264]
NPO16759	Polyalthia debilis	Species	Annonaceae	Eukaryota	Roots	n.a.	n.a.	PMID[20795741]
NPO11600	Scolopendra subspinipes	Species	Scolopendridae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12302	Hebanthe paniculata	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13233	Solanum megacarpum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12302	Hebanthe paniculata	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12135	Rhamnus triquetra	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11600	Scolopendra subspinipes	Species	Scolopendridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3396	Allium cernuum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16176	Citrus fusca	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16759	Polyalthia debilis	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15140	Soja max	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21487	Eunicea flexuosa	Species	Plexauridae	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 NPC137767 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	70
0.1-0.2	620
0.2-0.3	16592
0.3-0.4	17542
0.4-0.5	7119
0.5-0.6	705
0.6-0.7	47
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
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 NPC137767 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	75
0.1-0.2	397
0.2-0.3	3775
0.3-0.4	3786
0.4-0.5	979
0.5-0.6	138
0.6-0.7	0
0.7-0.8	0
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