NPASS Compound

Structure

NPC99931 OpenBabel06302216042D 27 29 0 0 1 0 0 0 0 0999 V2000 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 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 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 -2.5981 0.5000 0.0000 C 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 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 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 -2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 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 2 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 0.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 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 2 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 23 1 0 0 0 0 6 7 1 0 0 0 0 6 27 1 6 0 0 0 7 17 1 0 0 0 0 7 8 2 0 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 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 20 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 15 19 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 20 21 1 0 0 0 0 22 23 1 0 0 0 0 22 26 1 1 0 0 0 23 24 1 1 0 0 0 23 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	378.1
Volume:	354.872
LogP:	1.622
LogD:	1.07
LogS:	-3.425
# Rotatable Bonds:	3
TPSA:	153.75
# H-Bond Aceptor:	9
# H-Bond Donor:	5
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.378
Synthetic Accessibility Score:	3.995
Fsp3:	0.333
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.895
MDCK Permeability:	5.2253722060413565e-06
Pgp-inhibitor:	0.008
Pgp-substrate:	0.145
Human Intestinal Absorption (HIA):	0.91
20% Bioavailability (F20%):	0.023
30% Bioavailability (F30%):	0.856

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.024
Plasma Protein Binding (PPB):	90.64641571044922%
Volume Distribution (VD):	1.131
Pgp-substrate:	9.902665138244629%

ADMET: Metabolism

CYP1A2-inhibitor:	0.184
CYP1A2-substrate:	0.321
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.084
CYP2C9-inhibitor:	0.029
CYP2C9-substrate:	0.488
CYP2D6-inhibitor:	0.052
CYP2D6-substrate:	0.176
CYP3A4-inhibitor:	0.084
CYP3A4-substrate:	0.095

ADMET: Excretion

Clearance (CL):	1.057
Half-life (T1/2):	0.664

ADMET: Toxicity

hERG Blockers:	0.016
Human Hepatotoxicity (H-HT):	0.056
Drug-inuced Liver Injury (DILI):	0.943
AMES Toxicity:	0.451
Rat Oral Acute Toxicity:	0.018
Maximum Recommended Daily Dose:	0.024
Skin Sensitization:	0.224
Carcinogencity:	0.015
Eye Corrosion:	0.003
Eye Irritation:	0.112
Respiratory Toxicity:	0.052

Download Data

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

Natural Product: NPC99931

Natural Product ID:	NPC99931
*Common Name:**	JDGCLPKEFXLDSC-BDXSIMOUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JDGCLPKEFXLDSC-BDXSIMOUSA-N
Standard InCHI:	InChI=1S/C18H18O9/c1-6(19)27-17-15(23)11-12(16(24)18(17,2)25)13(21)8-4-7(26-3)5-9(20)10(8)14(11)22/h4-5,15-17,20,23-25H,1-3H3/t15-,16-,17+,18+/m1/s1
SMILES:	CC(=O)O[C@H]1[C@@H](C2=C(C(=O)c3cc(cc(c3C2=O)O)OC)[C@H]([C@]1(C)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	49822140
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones [CHEMONTID:0001598] Hydroxyanthraquinones

*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
NPO17255	Chondrosia corticata	Species	Chondrillidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15568783]
NPO16860	Stemphylium globuliferum	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19271717]
NPO16860	Stemphylium globuliferum	Species	Pleosporaceae	Eukaryota	Mentha pulegium	n.a.	n.a.	PMID[19271717]
NPO22865	Neopetrosia proxima	Species	Petrosiidae	Eukaryota	n.a.	Caribbean sea	n.a.	PMID[20727745]
NPO22865	Neopetrosia proxima	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21341726]
NPO17255	Chondrosia corticata	Species	Chondrillidae	Eukaryota	n.a.	reef slopes on the south side of Cocos Lagoon, Guam	n.a.	PMID[21550239]
NPO18542	Salvia sahendica	Species	Lamiaceae	Eukaryota	n.a.	collected from the plants natural habitat in Tabriz, Northwestern Iran, at an altitude of 1400 m	n.a.	PMID[21775156]
NPO16860	Stemphylium globuliferum	Species	Pleosporaceae	Eukaryota	Stems	n.a.	n.a.	PMID[23664494]
NPO16860	Stemphylium globuliferum	Species	Pleosporaceae	Eukaryota	isolated from fresh Juncus acutus	Lake Wadi el Natrun, Egypt	2012-NOV	PMID[25010124]
NPO18279	Paraconiothyrium brasiliense	Species	Didymosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25760674]
NPO18194	Primula modesta	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18194	Primula modesta	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18080	Peltophorum ferrugineum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17255	Chondrosia corticata	Species	Chondrillidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13444	Centaurea ptosimopappoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16860	Stemphylium globuliferum	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15888	Streptogonopus phipsoni	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO19726	Limnatis nilotica	Species	Hirudinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18542	Salvia sahendica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18944	Vernonia filigera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19101	Deutzia gracilis	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19382	Corallina elongata	Species	Corallinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19321	0tholaena californica	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18194	Primula modesta	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14894	Udotea conglutinata	Species	Udoteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22865	Neopetrosia proxima	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18279	Paraconiothyrium brasiliense	Species	Didymosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18687	Pterocarpus gracilis	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 NPC99931 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	360
0.1-0.2	1433
0.2-0.3	3323
0.3-0.4	7211
0.4-0.5	10352
0.5-0.6	4749
0.6-0.7	5151
0.7-0.8	6579
0.8-0.85	2946
0.85-0.9	520
0.9-0.95	66
0.95-1	7

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 NPC99931 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	312
0.1-0.2	919
0.2-0.3	1884
0.3-0.4	2520
0.4-0.5	1853
0.5-0.6	1036
0.6-0.7	422
0.7-0.8	162
0.8-0.85	36
0.85-0.9	6
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