NPASS Compound

Structure

NPC9661 OpenBabel06302215202D 43 48 0 0 1 0 0 0 0 0999 V2000 -1.7321 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 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 -1.7321 -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 -0.0000 -2.0000 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 -0.5000 0.0000 C 0 0 1 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 -1.7321 1.0000 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 -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 0.8660 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 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 C 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 2.5981 -0.5000 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 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 1.0000 0.0000 C 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 5.1962 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 4.0000 0.0000 O 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 0.0000 0.0000 0.0000 O 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 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 O 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 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 9 6 1 1 0 0 0 9 10 1 0 0 0 0 9 40 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 39 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 43 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 41 1 0 0 0 0 17 18 1 0 0 0 0 17 39 1 0 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 25 20 1 1 0 0 0 25 26 1 0 0 0 0 25 35 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 29 34 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 38 1 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 32 36 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 36 37 1 0 0 0 0 39 40 1 0 0 0 0 41 42 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	204.19
Volume:	239.69
LogP:	5.288
LogD:	4.932
LogS:	-5.05
# Rotatable Bonds:	1
TPSA:	0.0
# H-Bond Aceptor:	0
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	0

MedChem Properties

QED Drug-Likeness Score:	0.559
Synthetic Accessibility Score:	5.199
Fsp3:	0.867
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.269
MDCK Permeability:	2.169570689147804e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.892
30% Bioavailability (F30%):	0.904

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.287
Plasma Protein Binding (PPB):	96.51338958740234%
Volume Distribution (VD):	3.459
Pgp-substrate:	2.9077255725860596%

ADMET: Metabolism

CYP1A2-inhibitor:	0.789
CYP1A2-substrate:	0.48
CYP2C19-inhibitor:	0.445
CYP2C19-substrate:	0.897
CYP2C9-inhibitor:	0.413
CYP2C9-substrate:	0.192
CYP2D6-inhibitor:	0.04
CYP2D6-substrate:	0.495
CYP3A4-inhibitor:	0.431
CYP3A4-substrate:	0.462

ADMET: Excretion

Clearance (CL):	14.44
Half-life (T1/2):	0.106

ADMET: Toxicity

hERG Blockers:	0.044
Human Hepatotoxicity (H-HT):	0.207
Drug-inuced Liver Injury (DILI):	0.157
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.144
Maximum Recommended Daily Dose:	0.026
Skin Sensitization:	0.232
Carcinogencity:	0.051
Eye Corrosion:	0.929
Eye Irritation:	0.687
Respiratory Toxicity:	0.586

Download Data

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

Natural Product: NPC9661

Natural Product ID:	NPC9661
*Common Name:**	CFPJAFNVQKSAMP-KAYWLYCHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CFPJAFNVQKSAMP-KAYWLYCHSA-N
Standard InCHI:	InChI=1S/C33H28O10/c1-39-18-7-4-16(5-8-18)26-14-24(37)32-25(38)15-28(41-3)30(33(32)43-26)20-10-17(6-9-21(20)34)27-13-23(36)31-22(35)11-19(40-2)12-29(31)42-27/h4-12,15,26-27,34-35,38H,13-14H2,1-3H3/t26-,27-/m1/s1
SMILES:	COc1ccc(cc1)[C@H]1CC(=O)c2c(cc(c(c3cc(ccc3O)[C@H]3CC(=O)c4c(cc(cc4O3)OC)O)c2O1)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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
NPO4482	Leptosphaeria maculans	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18701303]
NPO4482	Leptosphaeria maculans	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22672981]
NPO7307	Exostema caribaeum	Species	Rubiaceae	Eukaryota	n.a.	mexican	n.a.	PMID[3204377]
NPO4482	Leptosphaeria maculans	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19858	Phyllophora nervosa	Species	Tettigoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO801	Aerva javanica	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4482	Leptosphaeria maculans	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2945	Lychnophora staavioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3918	Atergatis integerrimus	Species	Xanthidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15023	Pinus caribaea	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10850	Pseudochlorella pringsheimii	Species	Chlorellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7670	Eremurus sogdianus	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7307	Exostema caribaeum	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4850	Myrmicaria striata	Species	Formicidae	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 NPC9661 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	402
0.1-0.2	1533
0.2-0.3	3541
0.3-0.4	9241
0.4-0.5	9511
0.5-0.6	3584
0.6-0.7	5791
0.7-0.8	5103
0.8-0.85	2428
0.85-0.9	1119
0.9-0.95	391
0.95-1	53

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 NPC9661 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	349
0.1-0.2	932
0.2-0.3	1529
0.3-0.4	2607
0.4-0.5	1937
0.5-0.6	1150
0.6-0.7	429
0.7-0.8	164
0.8-0.85	32
0.85-0.9	16
0.9-0.95	5
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