NPASS Compound

Structure

NPC191259 OpenBabel06302216182D 35 37 0 0 1 0 0 0 0 0999 V2000 0.8660 -3.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 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 1.3660 -0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3660 -0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3660 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8660 -3.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 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 -1.0000 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 -0.6581 1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0683 2.0427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.2584 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 3.2584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.7584 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.7584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 5.2584 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 5.2584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3958 2.0427 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.8060 1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8060 0.7803 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7570 0.4712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5002 1.1404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9650 -0.5069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3958 0.2157 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.9836 -0.5934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7570 1.7872 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3364 1.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7431 0.6691 0.0000 N 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 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 1 1 0 0 0 3 5 1 0 0 0 0 3 11 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 11 35 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 30 1 0 0 0 0 14 15 2 0 0 0 0 15 35 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 33 2 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 18 24 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 24 25 2 3 0 0 0 25 26 1 0 0 0 0 25 32 1 0 0 0 0 26 27 1 1 0 0 0 26 30 1 0 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 30 31 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	479.31
Volume:	522.74
LogP:	5.707
LogD:	4.004
LogS:	-4.521
# Rotatable Bonds:	9
TPSA:	74.43
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.391
Synthetic Accessibility Score:	4.935
Fsp3:	0.517
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.831
MDCK Permeability:	1.3666290215041954e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.822
Human Intestinal Absorption (HIA):	0.076
20% Bioavailability (F20%):	0.521
30% Bioavailability (F30%):	0.207

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.687
Plasma Protein Binding (PPB):	93.93940734863281%
Volume Distribution (VD):	1.239
Pgp-substrate:	5.883066177368164%

ADMET: Metabolism

CYP1A2-inhibitor:	0.398
CYP1A2-substrate:	0.227
CYP2C19-inhibitor:	0.939
CYP2C19-substrate:	0.381
CYP2C9-inhibitor:	0.901
CYP2C9-substrate:	0.504
CYP2D6-inhibitor:	0.924
CYP2D6-substrate:	0.704
CYP3A4-inhibitor:	0.936
CYP3A4-substrate:	0.648

ADMET: Excretion

Clearance (CL):	2.718
Half-life (T1/2):	0.264

ADMET: Toxicity

hERG Blockers:	0.428
Human Hepatotoxicity (H-HT):	0.763
Drug-inuced Liver Injury (DILI):	0.411
AMES Toxicity:	0.067
Rat Oral Acute Toxicity:	0.324
Maximum Recommended Daily Dose:	0.894
Skin Sensitization:	0.618
Carcinogencity:	0.197
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.687

Download Data

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

Natural Product: NPC191259

Natural Product ID:	NPC191259
*Common Name:**	WUGMGNWGTQDXDH-NVLPUFGLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WUGMGNWGTQDXDH-NVLPUFGLSA-N
Standard InCHI:	InChI=1S/C29H41N3O3/c1-9-29(7,14-10-11-18(2)3)23-12-13-24-25-21(16-30-26(23)25)15-22(17-35-20(6)33)31-28(34)27(19(4)5)32(24)8/h9,11-13,16,19,22,27,30H,1,10,14-15,17H2,2-8H3,(H,31,34)/t22-,27-,29-/m0/s1
SMILES:	C=C[C@@](C)(CCC=C(C)C)c1ccc2c3c(C[C@@H](COC(=O)C)N=C([C@H](C(C)C)N2C)O)c[nH]c13
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10096667
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:0002309] Alpha amino acid amides

*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]
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]
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]

☑ 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 NPC191259 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	290
0.1-0.2	1756
0.2-0.3	16924
0.3-0.4	16139
0.4-0.5	3241
0.5-0.6	2403
0.6-0.7	1471
0.7-0.8	420
0.8-0.85	43
0.85-0.9	0
0.9-0.95	9
0.95-1	1

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 NPC191259 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	170
0.1-0.2	489
0.2-0.3	1002
0.3-0.4	1696
0.4-0.5	2734
0.5-0.6	2178
0.6-0.7	766
0.7-0.8	106
0.8-0.85	8
0.85-0.9	1
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