NPASS Compound

Structure

NPC170611 OpenBabel06302215222D 42 47 0 0 1 0 0 0 0 0999 V2000 1.0230 -4.4826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6802 -3.7518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6417 -3.9556 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3760 -2.8173 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.0332 -2.0865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4145 -2.6135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1103 -1.6790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8512 -1.4752 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.5084 -2.2060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8517 -0.4924 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.7029 -0.0010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7035 0.9822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0006 0.9832 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8512 1.4756 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8506 2.4594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7023 2.9518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5547 2.4604 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.5552 1.4766 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.4070 0.9852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2581 1.4776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2575 2.4614 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.4058 2.9528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4052 3.9594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2771 3.4569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1087 2.9538 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0920 2.9547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5829 3.8067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5844 2.1035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5677 2.1044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0602 1.2533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5692 0.4012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0616 -0.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0450 -0.4490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5359 0.4030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0435 1.2541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5374 -1.3002 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7035 0.9842 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7041 0.0010 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7046 -0.9828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8523 -0.4914 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0006 -1.0000 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 2 4 1 0 0 0 0 4 5 1 0 0 0 0 4 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 8 10 1 0 0 0 0 10 41 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 41 1 0 0 0 0 13 14 1 0 0 0 0 14 37 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 22 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 37 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 21 25 1 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 35 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 36 1 0 0 0 0 34 35 1 0 0 0 0 37 38 1 0 0 0 0 38 40 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 40 41 1 0 0 0 0 41 42 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	75.07
Volume:	80.231
LogP:	-2.076
LogD:	-1.739
LogS:	0.15
# Rotatable Bonds:	0
TPSA:	23.06
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.298
Synthetic Accessibility Score:	3.482
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.322
MDCK Permeability:	0.00015448121121153235
Pgp-inhibitor:	0.0
Pgp-substrate:	0.937
Human Intestinal Absorption (HIA):	0.836
20% Bioavailability (F20%):	0.86
30% Bioavailability (F30%):	0.621

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.389
Plasma Protein Binding (PPB):	9.192502975463867%
Volume Distribution (VD):	0.929
Pgp-substrate:	94.79793548583984%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.959
CYP2C19-inhibitor:	0.03
CYP2C19-substrate:	0.053
CYP2C9-inhibitor:	0.011
CYP2C9-substrate:	0.537
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.643
CYP3A4-inhibitor:	0.004
CYP3A4-substrate:	0.041

ADMET: Excretion

Clearance (CL):	8.189
Half-life (T1/2):	0.899

ADMET: Toxicity

hERG Blockers:	0.002
Human Hepatotoxicity (H-HT):	0.682
Drug-inuced Liver Injury (DILI):	0.016
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.033
Maximum Recommended Daily Dose:	0.076
Skin Sensitization:	0.019
Carcinogencity:	0.036
Eye Corrosion:	0.783
Eye Irritation:	0.854
Respiratory Toxicity:	0.012

Download Data

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

Natural Product: NPC170611

Natural Product ID:	NPC170611
*Common Name:**	KEZXVHCIQLIBOO-CIAFOILYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KEZXVHCIQLIBOO-CIAFOILYSA-N
Standard InCHI:	InChI=1S/C39H56O3/c1-23(2)24(3)8-9-25(4)31-18-19-33-29-15-17-32-28(37(29)30-22-34(30)39(31,33)7)16-20-35(38(32,5)6)42-36(41)21-12-26-10-13-27(40)14-11-26/h10-14,21,24-25,28-35,37,40H,1,8-9,15-20,22H2,2-7H3/b21-12+
SMILES:	C=C(C)C(C)CCC(C)C1CCC2C3CCC4C(CCC(C4(C)C)OC(=O)/C=C/c4ccc(cc4)O)C3C3CC3C12C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5320533
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001691] Steroid esters

*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
NPO25967	Mallotus philippensis	Species	Euphorbiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[12499591]
NPO25967	Mallotus philippensis	Species	Euphorbiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[15516755]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	leaves	n.a.	n.a.	PMID[15787442]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	n.a.	leaf	n.a.	PMID[15787442]
NPO21656	Pholidota yunnanensis	Species	Orchidaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[16394543]
NPO25967	Mallotus philippensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31318550]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[31809052]
NPO21656	Pholidota yunnanensis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25967	Mallotus philippensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21656	Pholidota yunnanensis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13961	Pieris japonica	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25967	Mallotus philippensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21656	Pholidota yunnanensis	Species	Orchidaceae	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 NPC170611 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	287
0.1-0.2	1366
0.2-0.3	2404
0.3-0.4	5106
0.4-0.5	10297
0.5-0.6	15583
0.6-0.7	6799
0.7-0.8	750
0.8-0.85	70
0.85-0.9	27
0.9-0.95	8
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 NPC170611 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	250
0.1-0.2	838
0.2-0.3	1344
0.3-0.4	2729
0.4-0.5	2265
0.5-0.6	1399
0.6-0.7	297
0.7-0.8	27
0.8-0.85	1
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