NPASS Compound

Structure

NPC87590 OpenBabel06302215382D 26 29 0 0 1 0 0 0 0 0999 V2000 -1.3271 2.2961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8417 1.4558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8414 0.4854 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6814 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5506 0.5007 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6811 -0.9713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 -0.9708 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8417 -1.4562 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8420 -2.4276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6834 -2.9131 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5245 -2.4271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3653 -2.9126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2059 -2.4267 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2056 -1.4553 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3648 -0.9698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5242 -1.4558 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5239 -0.4524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6828 -0.9703 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6825 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8411 0.4859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0003 1.0034 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0745 -0.9535 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0469 -2.9117 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.3473 -3.8350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6963 -2.1899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 21 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 21 1 0 0 0 0 8 9 1 1 0 0 0 8 18 1 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 16 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 24 1 6 0 0 0 14 15 1 0 0 0 0 14 23 1 1 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 16 18 1 0 0 0 0 18 19 1 6 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 6 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	359.28
Volume:	395.443
LogP:	3.572
LogD:	3.44
LogS:	-3.679
# Rotatable Bonds:	2
TPSA:	40.54
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.756
Synthetic Accessibility Score:	4.786
Fsp3:	0.87
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:	-4.628
MDCK Permeability:	1.2144767424615566e-05
Pgp-inhibitor:	0.964
Pgp-substrate:	0.446
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.287
30% Bioavailability (F30%):	0.194

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.992
Plasma Protein Binding (PPB):	62.3111572265625%
Volume Distribution (VD):	1.719
Pgp-substrate:	39.59084701538086%

ADMET: Metabolism

CYP1A2-inhibitor:	0.03
CYP1A2-substrate:	0.13
CYP2C19-inhibitor:	0.028
CYP2C19-substrate:	0.964
CYP2C9-inhibitor:	0.038
CYP2C9-substrate:	0.107
CYP2D6-inhibitor:	0.584
CYP2D6-substrate:	0.892
CYP3A4-inhibitor:	0.19
CYP3A4-substrate:	0.654

ADMET: Excretion

Clearance (CL):	18.316
Half-life (T1/2):	0.2

ADMET: Toxicity

hERG Blockers:	0.265
Human Hepatotoxicity (H-HT):	0.275
Drug-inuced Liver Injury (DILI):	0.434
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.817
Maximum Recommended Daily Dose:	0.884
Skin Sensitization:	0.231
Carcinogencity:	0.865
Eye Corrosion:	0.049
Eye Irritation:	0.017
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC87590

Natural Product ID:	NPC87590
*Common Name:**	YIGHZHOPCWHUCU-BPEWGCAGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YIGHZHOPCWHUCU-BPEWGCAGSA-N
Standard InCHI:	InChI=1S/C23H37NO2/c1-6-16-20(25)12-18-15-8-7-14-11-19(24(4)5)21(26)13-23(14,3)17(15)9-10-22(16,18)2/h7,15-19,21,26H,6,8-13H2,1-5H3/t15-,16+,17+,18+,19-,21-,22-,23+/m1/s1
SMILES:	CC[C@H]1C(=O)C[C@H]2[C@@H]3CC=C4C[C@H]([C@@H](C[C@]4(C)[C@H]3CC[C@]12C)O)N(C)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:0000258] Steroids and steroid derivatives [CHEMONTID:0003569] Pregnane steroids

*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
NPO4862	Westiellopsis prolifica	Species	Hapalosiphonaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1602299]
NPO11532	Bidens parviflora	Species	Asteraceae	Eukaryota	n.a.	whole plant	n.a.	PMID[16880667]
NPO14386	Piper hostmannianum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO13117	Asparagus setaceus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO765	Holarrhena pubescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6627	Pinus bungeana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10561	Mentha suaveolens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13117	Asparagus setaceus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6627	Pinus bungeana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11532	Bidens parviflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO765	Holarrhena pubescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO765	Holarrhena pubescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11073	Alpinia formosana	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14583	Elsholtzia stauntonii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9025	Croton balsamifer	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13993	Dimelaena thysanota	Species	Caliciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11532	Bidens parviflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12589	Heliotropium angiospermum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO805	Myrmicaria opaciventris	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13117	Asparagus setaceus	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14603	Flindersia australis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4862	Westiellopsis prolifica	Species	Hapalosiphonaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO765	Holarrhena pubescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21147	Anisocycla grandidieri	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13898	Typhonium flagelliforme	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1421	Papaver hybrid	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8641	Haemanthus tigrinus	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3577	Bambusa tulda	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11334	Rubus moluccanus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10561	Mentha suaveolens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6627	Pinus bungeana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10834	Protea compacta	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14386	Piper hostmannianum	Species	Piperaceae	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 NPC87590 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	85
0.1-0.2	643
0.2-0.3	4749
0.3-0.4	17909
0.4-0.5	9376
0.5-0.6	6621
0.6-0.7	2967
0.7-0.8	341
0.8-0.85	4
0.85-0.9	2
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 NPC87590 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	84
0.1-0.2	435
0.2-0.3	2897
0.3-0.4	3884
0.4-0.5	1228
0.5-0.6	363
0.6-0.7	217
0.7-0.8	42
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