NPASS Compound

Structure

NPC137240 OpenBabel06302216022D 33 34 0 0 1 0 0 0 0 0999 V2000 0.2288 -3.2436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6694 -3.5355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3712 -2.9035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2695 -3.1954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1749 -1.9797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8767 -1.3478 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6216 -1.3960 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8179 -0.4722 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7572 -0.3735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4590 0.2585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6554 1.1823 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2713 2.0451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4534 2.5173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5141 2.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1878 1.7866 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3841 0.8628 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3234 0.7641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7956 -0.0538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7076 1.6269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6314 1.8232 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0057 2.2588 0.0000 O 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 -1.4037 -1.2639 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3019 -0.9721 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4983 -0.0483 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0038 -1.6040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9020 -1.3122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0984 -0.3884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8074 -2.5278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6497 3.4411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1413 -1.2363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5862 -2.0004 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0806 -1.3350 0.0000 O 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 3 4 1 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 22 1 0 0 0 0 9 10 2 0 0 0 0 9 31 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 2 0 0 0 0 13 30 1 0 0 0 0 15 14 1 6 0 0 0 15 16 1 0 0 0 0 15 21 1 0 0 0 0 16 17 1 1 0 0 0 16 22 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 22 23 1 1 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 2 0 0 0 0 26 29 1 0 0 0 0 27 28 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	458.19
Volume:	470.437
LogP:	2.614
LogD:	1.589
LogS:	-3.15
# Rotatable Bonds:	7
TPSA:	116.2
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.288
Synthetic Accessibility Score:	5.314
Fsp3:	0.44
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.873
MDCK Permeability:	1.769149639585521e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.62
20% Bioavailability (F20%):	0.826
30% Bioavailability (F30%):	0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.224
Plasma Protein Binding (PPB):	85.3998031616211%
Volume Distribution (VD):	0.441
Pgp-substrate:	13.950800895690918%

ADMET: Metabolism

CYP1A2-inhibitor:	0.1
CYP1A2-substrate:	0.143
CYP2C19-inhibitor:	0.363
CYP2C19-substrate:	0.194
CYP2C9-inhibitor:	0.828
CYP2C9-substrate:	0.108
CYP2D6-inhibitor:	0.064
CYP2D6-substrate:	0.086
CYP3A4-inhibitor:	0.506
CYP3A4-substrate:	0.167

ADMET: Excretion

Clearance (CL):	6.394
Half-life (T1/2):	0.878

ADMET: Toxicity

hERG Blockers:	0.008
Human Hepatotoxicity (H-HT):	0.751
Drug-inuced Liver Injury (DILI):	0.942
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.404
Maximum Recommended Daily Dose:	0.057
Skin Sensitization:	0.295
Carcinogencity:	0.118
Eye Corrosion:	0.031
Eye Irritation:	0.148
Respiratory Toxicity:	0.851

Download Data

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

Natural Product: NPC137240

Natural Product ID:	NPC137240
*Common Name:**	GERKMQPROLJADS-KRLPWGDMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GERKMQPROLJADS-KRLPWGDMSA-N
Standard InCHI:	InChI=1S/C25H30O8/c1-7-14(4)23(28)32-20-17(22(26)27)11-9-10-13(3)12-18-19(16(6)25(30)31-18)21(20)33-24(29)15(5)8-2/h7-8,11-12,18-21H,6,9-10H2,1-5H3,(H,26,27)/b13-12-,14-7-,15-8-,17-11+/t18-,19+,20+,21+/m1/s1
SMILES:	C/C=C(/C)C(=O)O[C@H]1/C(=CCC/C(=C[C@@H]2[C@H](C(=C)C(=O)O2)[C@@H]1OC(=O)/C(=CC)/C)/C)/C(=O)O
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:0001283] Terpene lactones [CHEMONTID:0001543] Sesquiterpene lactones [CHEMONTID:0001771] Germacranolides 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
NPO28966	Trichoderma longibrachiatum	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11429993]
NPO28644	Cladiella australis	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16038547]
NPO29119	Nepenthes thorelii	Species	Nepenthaceae	Eukaryota	roots	n.a.	n.a.	PMID[19299148]
NPO29119	Nepenthes thorelii	Species	Nepenthaceae	Eukaryota	n.a.	root	n.a.	PMID[9581522]
NPO28966	Trichoderma longibrachiatum	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO29166	Gymnema sylvestre	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25423	Gardenia thailandica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29166	Gymnema sylvestre	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29166	Gymnema sylvestre	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10189	Abutilon theophrasti	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28730	Ranunculus sardous	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29119	Nepenthes thorelii	Species	Nepenthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28966	Trichoderma longibrachiatum	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10189	Abutilon theophrasti	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28644	Cladiella australis	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29023	Audouinia tentaculata	Species	Bruniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29166	Gymnema sylvestre	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25423	Gardenia thailandica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28913	Hedychium villosum	Species	Zingiberaceae	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 NPC137240 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	201
0.1-0.2	1352
0.2-0.3	4838
0.3-0.4	8458
0.4-0.5	15190
0.5-0.6	7604
0.6-0.7	3770
0.7-0.8	1035
0.8-0.85	159
0.85-0.9	73
0.9-0.95	15
0.95-1	2

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 NPC137240 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	189
0.1-0.2	1993
0.2-0.3	3671
0.3-0.4	2146
0.4-0.5	787
0.5-0.6	290
0.6-0.7	62
0.7-0.8	11
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