NPASS Compound

Structure

NPC93929 OpenBabel06302216062D 25 28 0 0 1 0 0 0 0 0999 V2000 -7.3250 2.2237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9182 1.3102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9237 1.2056 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5170 0.2921 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3830 0.7921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2490 0.2921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2490 -0.7079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1151 -1.2079 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3830 -1.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5170 -0.7079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5659 -1.0169 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9781 -0.2079 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5659 0.6011 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2569 1.5522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9781 -0.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4781 -1.0739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4781 -1.0739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9781 -0.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4781 0.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4781 0.6581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 1.4013 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1045 0.9945 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 -8.1151 0.7921 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.9811 0.2921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 4 3 1 6 0 0 0 4 13 1 0 0 0 0 4 5 1 0 0 0 0 4 10 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 6 24 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 10 2 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 12 15 1 1 0 0 0 13 14 1 6 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 23 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	340.13
Volume:	345.746
LogP:	3.107
LogD:	2.854
LogS:	-4.662
# Rotatable Bonds:	4
TPSA:	53.99
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.783
Synthetic Accessibility Score:	4.254
Fsp3:	0.35
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.789
MDCK Permeability:	2.33912724070251e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.978
30% Bioavailability (F30%):	0.857

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.058
Plasma Protein Binding (PPB):	95.91333770751953%
Volume Distribution (VD):	0.864
Pgp-substrate:	3.4755992889404297%

ADMET: Metabolism

CYP1A2-inhibitor:	0.928
CYP1A2-substrate:	0.728
CYP2C19-inhibitor:	0.964
CYP2C19-substrate:	0.797
CYP2C9-inhibitor:	0.866
CYP2C9-substrate:	0.738
CYP2D6-inhibitor:	0.977
CYP2D6-substrate:	0.515
CYP3A4-inhibitor:	0.972
CYP3A4-substrate:	0.682

ADMET: Excretion

Clearance (CL):	13.355
Half-life (T1/2):	0.363

ADMET: Toxicity

hERG Blockers:	0.071
Human Hepatotoxicity (H-HT):	0.8
Drug-inuced Liver Injury (DILI):	0.095
AMES Toxicity:	0.026
Rat Oral Acute Toxicity:	0.629
Maximum Recommended Daily Dose:	0.714
Skin Sensitization:	0.808
Carcinogencity:	0.834
Eye Corrosion:	0.007
Eye Irritation:	0.067
Respiratory Toxicity:	0.948

Download Data

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

Natural Product: NPC93929

Natural Product ID:	NPC93929
*Common Name:**	SOLJFAQVSWXZEQ-CFGAKRJMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SOLJFAQVSWXZEQ-CFGAKRJMSA-N
Standard InCHI:	InChI=1S/C20H20O5/c1-4-7-20-10-17(22-3)14(21)9-18(20)25-19(12(20)2)13-5-6-15-16(8-13)24-11-23-15/h4-6,8-10,12,19H,1,7,11H2,2-3H3/t12-,19+,20+/m1/s1
SMILES:	C=CC[C@]12C=C(C(=O)C=C2O[C@@H]([C@H]1C)c1ccc2c(c1)OCO2)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10903924
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003405] 2-arylbenzofuran flavonoids

*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
NPO16425	Bupleurum longiradiatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19994846]
NPO16953	Piper wallichii	Species	Piperaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[20394289]
NPO16953	Piper wallichii	Species	Piperaceae	Eukaryota	n.a.	stem	n.a.	PMID[22734410]
NPO26543	Ocotea cymbarum	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24713267]
NPO16953	Piper wallichii	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2609983]
NPO27735	Aniba citrifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31577436]
NPO16425	Bupleurum longiradiatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16953	Piper wallichii	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9078	Piper hancei	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16953	Piper wallichii	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16425	Bupleurum longiradiatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9078	Piper hancei	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16425	Bupleurum longiradiatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26543	Ocotea cymbarum	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9078	Piper hancei	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27735	Aniba citrifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16953	Piper wallichii	Species	Piperaceae	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

Activity Type	# Activity
IC50	2

Activity Type	# Activity
Cell Line	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT179	Cell Line	A2780	Homo sapiens	IC50	>	10000.0	nM	PMID[31577436]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	>	30000.0	nM	PMID[31577436]

☑ 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 NPC93929 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	436
0.1-0.2	1415
0.2-0.3	3278
0.3-0.4	8379
0.4-0.5	10900
0.5-0.6	5666
0.6-0.7	10508
0.7-0.8	1924
0.8-0.85	157
0.85-0.9	26
0.9-0.95	5
0.95-1	3

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 NPC93929 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	343
0.1-0.2	861
0.2-0.3	1771
0.3-0.4	2754
0.4-0.5	1917
0.5-0.6	1038
0.6-0.7	432
0.7-0.8	33
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