NPASS Compound

Structure

NPC167667 OpenBabel06302215082D 38 42 0 0 1 0 0 0 0 0999 V2000 -4.8036 -2.5593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8091 -2.6638 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2213 -1.8548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6281 -0.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0403 -0.1322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0458 -0.2368 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6390 -1.1503 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2268 -1.9593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6445 -1.0458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4366 -0.0676 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4294 -0.5676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4294 -1.5676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2954 -2.0676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1615 -1.5676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1615 -0.5676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2954 -0.0676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0275 -0.0676 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0275 0.9324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0275 -2.0676 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8935 -1.5676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3065 0.6015 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2847 0.3936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5937 -0.5575 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5719 -0.7654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2410 -0.0222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9320 0.9288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9538 1.1367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1002 1.5150 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0947 1.4105 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3026 0.4324 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1687 0.9324 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7638 2.1537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 0.0000 0.0000 O 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 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4470 0.7813 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8592 1.5903 0.0000 C 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 5 37 1 0 0 0 0 6 30 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 9 10 1 0 0 0 0 10 30 1 0 0 0 0 10 11 1 1 0 0 0 10 21 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 14 15 2 0 0 0 0 14 19 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 1 0 0 0 21 28 1 0 0 0 0 22 27 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 28 29 1 0 0 0 0 28 33 1 6 0 0 0 29 30 1 0 0 0 0 29 32 1 6 0 0 0 30 31 1 1 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 35 36 1 0 0 0 0 37 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	522.19
Volume:	520.105
LogP:	3.224
LogD:	3.09
LogS:	-4.96
# Rotatable Bonds:	8
TPSA:	112.91
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.452
Synthetic Accessibility Score:	3.993
Fsp3:	0.345
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.317
MDCK Permeability:	5.355215398594737e-05
Pgp-inhibitor:	0.996
Pgp-substrate:	0.026
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.652

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.641
Plasma Protein Binding (PPB):	78.10514068603516%
Volume Distribution (VD):	1.152
Pgp-substrate:	12.952589988708496%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.891
CYP2C19-inhibitor:	0.342
CYP2C19-substrate:	0.882
CYP2C9-inhibitor:	0.38
CYP2C9-substrate:	0.471
CYP2D6-inhibitor:	0.02
CYP2D6-substrate:	0.897
CYP3A4-inhibitor:	0.955
CYP3A4-substrate:	0.911

ADMET: Excretion

Clearance (CL):	8.894
Half-life (T1/2):	0.412

ADMET: Toxicity

hERG Blockers:	0.214
Human Hepatotoxicity (H-HT):	0.504
Drug-inuced Liver Injury (DILI):	0.29
AMES Toxicity:	0.131
Rat Oral Acute Toxicity:	0.365
Maximum Recommended Daily Dose:	0.451
Skin Sensitization:	0.027
Carcinogencity:	0.066
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.681

Download Data

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

Natural Product: NPC167667

Natural Product ID:	NPC167667
*Common Name:**	OWHOEKLNSDNYTQ-IDAMAFBJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OWHOEKLNSDNYTQ-IDAMAFBJSA-N
Standard InCHI:	InChI=1S/C29H30O9/c1-33-18-14-21(36-4)25-22(15-18)38-29(17-11-12-19(34-2)20(13-17)35-3)24(16-9-7-6-8-10-16)23(27(31)37-5)26(30)28(25,29)32/h6-15,23-24,26,30,32H,1-5H3/t23-,24-,26-,28+,29+/m1/s1
SMILES:	COc1cc(c2c(c1)O[C@@]1(c3ccc(c(c3)OC)OC)[C@H](c3ccccc3)[C@H]([C@H]([C@@]21O)O)C(=O)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10720804
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000301] Benzofurans [CHEMONTID:0003109] Flavaglines

*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
NPO993	Phaseolus coccineus	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO993	Phaseolus coccineus	Species	Fabaceae	Eukaryota	Leaf Diffusate	n.a.	n.a.	Database[FooDB]
NPO993	Phaseolus coccineus	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO993	Phaseolus coccineus	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO27623	Citrus japonica	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO993	Phaseolus coccineus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19682	Duguetia chrysocarpa	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20667	Cereus queretaroensis	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22318	Sechium edule	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13294	Pinus yunnanensis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18179	Leucopaxillus amarus	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21632	Chlorobium phaeovibrioides	Species	Chlorobiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO993	Phaseolus coccineus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20222	Franseria ambrosioides	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO23171	Hygrophorus olivaceoalbus	Species	Hygrophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23092	Ammodendron karelinii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28052	Miriquidica leucophaea	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27623	Citrus japonica	Species	Rutaceae	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 NPC167667 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	370
0.1-0.2	1430
0.2-0.3	3217
0.3-0.4	7090
0.4-0.5	10892
0.5-0.6	5340
0.6-0.7	5989
0.7-0.8	7904
0.8-0.85	433
0.85-0.9	18
0.9-0.95	5
0.95-1	9

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 NPC167667 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	842
0.2-0.3	1870
0.3-0.4	2556
0.4-0.5	1984
0.5-0.6	980
0.6-0.7	477
0.7-0.8	117
0.8-0.85	10
0.85-0.9	2
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