NPASS Compound

Structure

NPC126064 OpenBabel06302215332D 29 31 0 0 1 0 0 0 0 0999 V2000 -1.9603 6.8120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7015 5.8461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4086 5.1390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1498 4.1730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8569 3.4659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3914 1.8912 0.0000 C 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 -1.7321 1.0000 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 -0.0000 1.0000 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 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 4.0000 0.0000 O 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 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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 O 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 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7356 5.5872 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 29 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 16 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 22 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 19 2 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 19 28 1 0 0 0 0 20 21 2 0 0 0 0 20 25 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 25 26 2 0 0 0 0 25 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	398.17
Volume:	412.344
LogP:	5.836
LogD:	3.602
LogS:	-3.797
# Rotatable Bonds:	6
TPSA:	85.22
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.653
Synthetic Accessibility Score:	3.491
Fsp3:	0.348
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.771
MDCK Permeability:	1.507419437984936e-05
Pgp-inhibitor:	0.055
Pgp-substrate:	0.019
Human Intestinal Absorption (HIA):	0.032
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.014
Plasma Protein Binding (PPB):	85.74169158935547%
Volume Distribution (VD):	0.67
Pgp-substrate:	15.098516464233398%

ADMET: Metabolism

CYP1A2-inhibitor:	0.13
CYP1A2-substrate:	0.828
CYP2C19-inhibitor:	0.042
CYP2C19-substrate:	0.359
CYP2C9-inhibitor:	0.384
CYP2C9-substrate:	0.315
CYP2D6-inhibitor:	0.726
CYP2D6-substrate:	0.143
CYP3A4-inhibitor:	0.165
CYP3A4-substrate:	0.13

ADMET: Excretion

Clearance (CL):	4.286
Half-life (T1/2):	0.564

ADMET: Toxicity

hERG Blockers:	0.034
Human Hepatotoxicity (H-HT):	0.909
Drug-inuced Liver Injury (DILI):	0.98
AMES Toxicity:	0.091
Rat Oral Acute Toxicity:	0.69
Maximum Recommended Daily Dose:	0.187
Skin Sensitization:	0.13
Carcinogencity:	0.446
Eye Corrosion:	0.003
Eye Irritation:	0.063
Respiratory Toxicity:	0.575

Download Data

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

Natural Product: NPC126064

Natural Product ID:	NPC126064
*Common Name:**	NDQMIKVRLVQYOQ-HSZRJFAPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NDQMIKVRLVQYOQ-HSZRJFAPSA-N
Standard InCHI:	InChI=1S/C23H26O6/c1-13(2)7-6-9-23(3)10-8-14-19-15(11-18(28-5)21(14)29-23)20(24)16(22(25)26)12-17(19)27-4/h7-8,10-12,24H,6,9H2,1-5H3,(H,25,26)/t23-/m1/s1
SMILES:	CC(=CCC[C@]1(C)C=Cc2c3c(cc(c2O1)OC)c(c(cc3OC)C(=O)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001640] Naphthopyrans

*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
NPO7587	Mallotus resinosus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15387675]
NPO15231	Axinella damicornis	Species	Axinellidae	Eukaryota	n.a.	Mediterranean	n.a.	PMID[17582775]
NPO6195	Rhodopentas bussei	Species	Rubiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[27518587]
NPO21314	Trametes sanguinea	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7587	Mallotus resinosus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2522	Fannia femoralis	Species	Fanniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1433	Hepialus californicus	Species	Hepialidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4718	Daphne sericea	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11743	Phryxe caudata	Species	Tachinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15231	Axinella damicornis	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12699	Cronartium fusiforme	Species	Cronartiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4641	Baccharis nitida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10390	Orbexilum onobrychis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12803	Leuzea longifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21314	Trametes sanguinea	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6195	Rhodopentas bussei	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2973	Euphorbia bungei	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8158	Euchresta horsfieldii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3514.1	Klebsiella pneumoniae subsp. ozaenae	Subspecies	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO4906	Streptomyces flavoviridis	Species	Streptomycetaceae	Bacteria	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 NPC126064 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	385
0.1-0.2	1630
0.2-0.3	3784
0.3-0.4	8924
0.4-0.5	9228
0.5-0.6	3291
0.6-0.7	5492
0.7-0.8	7364
0.8-0.85	2174
0.85-0.9	400
0.9-0.95	23
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 NPC126064 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	352
0.1-0.2	972
0.2-0.3	1637
0.3-0.4	2555
0.4-0.5	1847
0.5-0.6	1036
0.6-0.7	518
0.7-0.8	202
0.8-0.85	26
0.85-0.9	5
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