NPASS Compound

Structure

NPC115537 OpenBabel06302215262D 30 33 0 0 1 0 0 0 0 0999 V2000 0.4750 3.1646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0775 2.8168 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0775 2.1211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4751 1.7733 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1274 2.1211 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4751 1.0776 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1273 0.4751 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4751 -0.1273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3564 -0.1273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9502 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8228 -1.4253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6457 -0.9502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6458 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4687 0.4751 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4686 -0.4468 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2915 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1144 0.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1144 1.4252 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2916 1.9003 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8306 2.6987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4687 1.4252 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6458 1.9003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8229 1.4253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8229 0.4751 0.0000 C 0 0 2 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 -3.7525 2.6987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2916 3.4971 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6744 2.6987 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1354 3.4971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6800 3.1646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 30 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 7 6 1 1 0 0 0 7 8 1 0 0 0 0 7 24 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 6 0 0 0 10 25 1 0 0 0 0 11 12 1 0 0 0 0 13 12 1 1 0 0 0 13 14 1 0 0 0 0 13 24 1 0 0 0 0 14 21 1 0 0 0 0 14 15 1 1 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 6 0 0 0 19 21 1 0 0 0 0 19 26 1 0 0 0 0 21 22 1 1 0 0 0 22 23 1 0 0 0 0 24 23 1 1 0 0 0 24 25 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	414.28
Volume:	448.641
LogP:	4.986
LogD:	4.105
LogS:	-5.633
# Rotatable Bonds:	5
TPSA:	52.6
# H-Bond Aceptor:	4
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.342
Synthetic Accessibility Score:	5.762
Fsp3:	0.769
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:	-4.785
MDCK Permeability:	2.4215118173742667e-05
Pgp-inhibitor:	0.991
Pgp-substrate:	0.012
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.176
30% Bioavailability (F30%):	0.796

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.666
Plasma Protein Binding (PPB):	83.59439086914062%
Volume Distribution (VD):	1.475
Pgp-substrate:	9.267265319824219%

ADMET: Metabolism

CYP1A2-inhibitor:	0.242
CYP1A2-substrate:	0.509
CYP2C19-inhibitor:	0.687
CYP2C19-substrate:	0.802
CYP2C9-inhibitor:	0.777
CYP2C9-substrate:	0.043
CYP2D6-inhibitor:	0.291
CYP2D6-substrate:	0.149
CYP3A4-inhibitor:	0.952
CYP3A4-substrate:	0.363

ADMET: Excretion

Clearance (CL):	5.826
Half-life (T1/2):	0.051

ADMET: Toxicity

hERG Blockers:	0.073
Human Hepatotoxicity (H-HT):	0.532
Drug-inuced Liver Injury (DILI):	0.799
AMES Toxicity:	0.078
Rat Oral Acute Toxicity:	0.924
Maximum Recommended Daily Dose:	0.953
Skin Sensitization:	0.912
Carcinogencity:	0.724
Eye Corrosion:	0.912
Eye Irritation:	0.725
Respiratory Toxicity:	0.953

Download Data

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

Natural Product: NPC115537

Natural Product ID:	NPC115537
*Common Name:**	WDKAHRJFGRACDV-BYCYOMRWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WDKAHRJFGRACDV-BYCYOMRWSA-N
Standard InCHI:	InChI=1S/C26H38O4/c1-16(2)14-21(27)30-22-17(3)18-8-9-20-24(4)11-7-12-25(5,23(28)29-6)19(24)10-13-26(20,22)15-18/h14,18-20,22H,3,7-13,15H2,1-2,4-6H3/t18-,19+,20+,22+,24-,25-,26-/m1/s1
SMILES:	CC(=CC(=O)O[C@H]1C(=C)[C@@H]2CC[C@H]3[C@]4(C)CCC[C@](C)([C@H]4CC[C@]13C2)C(=O)OC)C
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:0001551] Diterpenoids [CHEMONTID:0003782] Kaurane diterpenoids

*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
NPO13461	Maytenus buchananii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075788]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18321057]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[19099222]
NPO13162	Glycosmis petelotii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24949913]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30724086]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31550154]
NPO13461	Maytenus buchananii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7463095]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13461	Maytenus buchananii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13461	Maytenus buchananii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5896	Crinum laurentii	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13461	Maytenus buchananii	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13162	Glycosmis petelotii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26146	Ruilopezia lindenii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15995	Moesziomyces rugulosus	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12829	Ocotea acutifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12682	Euphorbia helioscopia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12346	Daphnandra apatela	Species	Atherospermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5896	Crinum laurentii	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9211	Margyricarpus setosus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10762	Brasilia sickii	n.a.	n.a.	n.a.	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 NPC115537 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	204
0.1-0.2	1345
0.2-0.3	5483
0.3-0.4	14327
0.4-0.5	7165
0.5-0.6	6757
0.6-0.7	5687
0.7-0.8	1662
0.8-0.85	60
0.85-0.9	4
0.9-0.95	2
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 NPC115537 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	172
0.1-0.2	1594
0.2-0.3	4030
0.3-0.4	2265
0.4-0.5	619
0.5-0.6	191
0.6-0.7	176
0.7-0.8	84
0.8-0.85	18
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