NPASS Compound

Structure

NPC93462 OpenBabel06302215282D 34 38 0 0 1 0 0 0 0 0999 V2000 0.8438 1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8438 0.4872 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6876 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6876 -0.9744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8438 -1.4615 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6876 -1.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8438 -2.4359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.9231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8438 -2.4359 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8438 -4.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8438 -1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6876 -0.9744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5315 -1.4615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5315 -2.4359 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3753 -2.9231 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3753 -1.9487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2191 -2.4359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0629 -2.9231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0629 -3.8974 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2191 -4.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7063 -5.2284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7319 -5.2284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3753 -3.8974 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5315 -4.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6876 -3.8974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6876 -2.9231 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8438 -3.4103 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9067 -4.3846 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7506 -3.8974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7506 -2.9231 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5944 -4.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9744 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8438 0.4872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 33 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 32 1 0 0 0 0 5 6 1 1 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 26 1 0 0 0 0 9 10 1 1 0 0 0 9 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 26 1 0 0 0 0 15 23 1 0 0 0 0 15 16 1 1 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 28 1 1 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 1 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 1 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 32 11 1 1 0 0 0 32 33 1 0 0 0 0 33 34 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	468.4
Volume:	531.553
LogP:	7.714
LogD:	5.884
LogS:	-7.199
# Rotatable Bonds:	2
TPSA:	26.3
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.284
Synthetic Accessibility Score:	4.721
Fsp3:	0.906
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.865
MDCK Permeability:	9.489200238022022e-06
Pgp-inhibitor:	0.278
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.978
30% Bioavailability (F30%):	0.864

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.121
Plasma Protein Binding (PPB):	96.9909896850586%
Volume Distribution (VD):	1.648
Pgp-substrate:	1.6349915266036987%

ADMET: Metabolism

CYP1A2-inhibitor:	0.046
CYP1A2-substrate:	0.215
CYP2C19-inhibitor:	0.106
CYP2C19-substrate:	0.943
CYP2C9-inhibitor:	0.167
CYP2C9-substrate:	0.189
CYP2D6-inhibitor:	0.088
CYP2D6-substrate:	0.637
CYP3A4-inhibitor:	0.526
CYP3A4-substrate:	0.705

ADMET: Excretion

Clearance (CL):	3.928
Half-life (T1/2):	0.031

ADMET: Toxicity

hERG Blockers:	0.045
Human Hepatotoxicity (H-HT):	0.123
Drug-inuced Liver Injury (DILI):	0.401
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.144
Maximum Recommended Daily Dose:	0.785
Skin Sensitization:	0.687
Carcinogencity:	0.025
Eye Corrosion:	0.957
Eye Irritation:	0.763
Respiratory Toxicity:	0.91

Download Data

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

Natural Product: NPC93462

Natural Product ID:	NPC93462
*Common Name:**	UDXDFWBZZQHDRO-NGIVGADOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UDXDFWBZZQHDRO-NGIVGADOSA-N
Standard InCHI:	InChI=1S/C32H52O2/c1-20-12-15-29(6)18-19-31(8)23(27(29)21(20)2)10-11-25-30(7)16-14-26(34-22(3)33)28(4,5)24(30)13-17-32(25,31)9/h10,20-21,24-27H,11-19H2,1-9H3/t20-,21+,24+,25+,26+,27-,29-,30+,31+,32-/m1/s1
SMILES:	C[C@@H]1CC[C@]2(C)CC[C@@]3(C)C(=CC[C@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]34C)OC(=O)C)[C@H]2[C@H]1C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO22460	Vernonia pachyclada	Species	Asteraceae	Eukaryota	n.a.	Madagascar rainforest	n.a.	PMID[16180816]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19388660]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21524573]
NPO12737.1	Torreya fargesii var. yunnanensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25495612]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28362501]
NPO15473	Ocotea heterochroma	Species	Lauraceae	Eukaryota	leaves	n.a.	n.a.	PMID[30188730]
NPO17949	Gentiana thunbergii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29082	Persicaria hydropiper	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12737.1	Torreya fargesii var. yunnanensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20969	Pseudognaphalium affine	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17949	Gentiana thunbergii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15971	Teclea boiviniana	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22460	Vernonia pachyclada	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2709	Flindersia dissosperma	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17032	Knautia silvatica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17792	Penicillium lapidosum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12737.1	Torreya fargesii var. yunnanensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16515	Siphonoglossa mexicana	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO17875	Erythroxylum microphyllum	Species	Erythroxylaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29082	Persicaria hydropiper	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17407	Bauhinia splendens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17105	Phaenocoma prolifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14133	Eupatorium perfoliatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26459	Lissoclinum fragile	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15473	Ocotea heterochroma	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20969	Pseudognaphalium affine	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16738	Leptogorgia gilchristi	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17949	Gentiana thunbergii	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17640	Omphalotus nidiformis	Species	Omphalotaceae	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 NPC93462 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	212
0.1-0.2	1749
0.2-0.3	6669
0.3-0.4	16706
0.4-0.5	6814
0.5-0.6	5061
0.6-0.7	4180
0.7-0.8	993
0.8-0.85	224
0.85-0.9	68
0.9-0.95	14
0.95-1	7

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 NPC93462 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	204
0.1-0.2	1951
0.2-0.3	4250
0.3-0.4	1946
0.4-0.5	430
0.5-0.6	243
0.6-0.7	109
0.7-0.8	11
0.8-0.85	3
0.85-0.9	3
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