NPASS Compound

Structure

NPC207078 OpenBabel06302216192D 42 42 0 0 0 0 0 0 0 0999 V2000 -10.3923 -22.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -22.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -22.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -21.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -19.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -19.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -18.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -17.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -16.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -16.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 O 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 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 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 -0.8660 0.5000 0.0000 C 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 -1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 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 14 15 1 0 0 0 0 15 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 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 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 32 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 34 39 2 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 36 37 1 0 0 0 0 37 38 2 0 0 0 0 37 41 1 0 0 0 0 38 39 1 0 0 0 0 38 40 1 0 0 0 0 41 42 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	586.5
Volume:	679.226
LogP:	13.104
LogD:	5.112
LogS:	-7.53
# Rotatable Bonds:	31
TPSA:	55.76
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.055
Synthetic Accessibility Score:	2.547
Fsp3:	0.763
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.494
MDCK Permeability:	3.2844113775354344e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	102.00729370117188%
Volume Distribution (VD):	6.042
Pgp-substrate:	0.4757634401321411%

ADMET: Metabolism

CYP1A2-inhibitor:	0.042
CYP1A2-substrate:	0.125
CYP2C19-inhibitor:	0.14
CYP2C19-substrate:	0.045
CYP2C9-inhibitor:	0.029
CYP2C9-substrate:	0.997
CYP2D6-inhibitor:	0.192
CYP2D6-substrate:	0.095
CYP3A4-inhibitor:	0.183
CYP3A4-substrate:	0.022

ADMET: Excretion

Clearance (CL):	4.287
Half-life (T1/2):	0.026

ADMET: Toxicity

hERG Blockers:	0.332
Human Hepatotoxicity (H-HT):	0.004
Drug-inuced Liver Injury (DILI):	0.767
AMES Toxicity:	0.017
Rat Oral Acute Toxicity:	0.006
Maximum Recommended Daily Dose:	0.025
Skin Sensitization:	0.987
Carcinogencity:	0.022
Eye Corrosion:	0.86
Eye Irritation:	0.932
Respiratory Toxicity:	0.224

Download Data

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

Natural Product: NPC207078

Natural Product ID:	NPC207078
*Common Name:**	XEOWPOLWKNHXGL-NHQGMKOOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XEOWPOLWKNHXGL-NHQGMKOOSA-N
Standard InCHI:	InChI=1S/C38H66O4/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27-28-33-42-38(40)32-30-35-29-31-37(41-2)36(39)34-35/h29-32,34,39H,3-28,33H2,1-2H3/b32-30+
SMILES:	CCCCCCCCCCCCCCCCCCCCCCCCCCCCOC(=O)/C=C/c1ccc(c(c1)O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101426086
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0000059] Coumaric acids and derivatives

*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
NPO29113	Erythrina vogelii	Species	Fabaceae	Eukaryota	root bark	n.a.	n.a.	PMID[11908991]
NPO27807	Calotropis procera	Species	Apocynaceae	Eukaryota	root barks	n.a.	n.a.	PMID[15689169]
NPO28587	Axinella weltneri	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[16124780]
NPO28764	Phyllidia ocellata	Species	Phyllidiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[26056748]
NPO28587	Axinella weltneri	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[9249974]
NPO29113	Erythrina vogelii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29113	Erythrina vogelii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28553	Nannoglottis ravida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27807	Calotropis procera	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29056	Dactynotus ambrosiae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO28640	Alsidium corallinum	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28436	Helenium virginicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28587	Axinella weltneri	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO28944	Heliotropium digynum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28764	Phyllidia ocellata	Species	Phyllidiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29181	Galdieria sulphuraria	Species	Cyanidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28535	Astragalus flexus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5436	Absidia caerulea	Species	Cunninghamellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27807	Calotropis procera	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28517	Hypericum caprifoliatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27459	Balanophora tobiracola	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28553	Nannoglottis ravida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22444	Ceramium boydenii	Species	Ceramiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28399	Anthotroche myoporoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25617	Lactococcus lactis	Species	Streptococcaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO29113	Erythrina vogelii	Species	Fabaceae	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 NPC207078 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	249
0.1-0.2	1352
0.2-0.3	4266
0.3-0.4	10477
0.4-0.5	7823
0.5-0.6	4806
0.6-0.7	9935
0.7-0.8	3213
0.8-0.85	405
0.85-0.9	136
0.9-0.95	24
0.95-1	11

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 NPC207078 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	228
0.1-0.2	878
0.2-0.3	1759
0.3-0.4	2666
0.4-0.5	1775
0.5-0.6	1046
0.6-0.7	697
0.7-0.8	95
0.8-0.85	4
0.85-0.9	2
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