NPASS Compound

Structure

NPC79523 OpenBabel06302216022D 30 31 0 0 1 0 0 0 0 0999 V2000 -1.6685 0.1346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9979 0.8764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0201 0.6665 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2718 1.2661 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8089 1.6613 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4262 2.5852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4681 1.7616 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0486 2.6694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0985 1.5441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6415 2.3839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5556 1.0586 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7346 0.4162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5947 -0.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5947 0.7642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8876 1.4713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8876 1.4713 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.5049 2.3952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1805 0.7642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1805 -0.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8876 -0.9429 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8876 -0.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2703 -1.8668 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3276 -0.5808 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 -0.9633 -0.2685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0445 2.5789 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4964 1.9063 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3261 2.8917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0943 3.5319 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6125 3.2369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 1 0 0 0 3 4 1 0 0 0 0 3 24 1 0 0 0 0 4 5 1 0 0 0 0 4 27 1 6 0 0 0 5 6 1 1 0 0 0 5 7 1 0 0 0 0 7 8 1 6 0 0 0 7 9 1 0 0 0 0 7 26 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 21 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 20 19 1 1 0 0 0 20 21 1 0 0 0 0 20 23 1 0 0 0 0 21 22 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 28 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	425.2
Volume:	422.796
LogP:	1.015
LogD:	-0.078
LogS:	-2.136
# Rotatable Bonds:	3
TPSA:	119.44
# H-Bond Aceptor:	9
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.507
Synthetic Accessibility Score:	6.038
Fsp3:	0.714
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.929
MDCK Permeability:	8.278853056253865e-05
Pgp-inhibitor:	0.962
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.422
20% Bioavailability (F20%):	0.046
30% Bioavailability (F30%):	0.957

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.371
Plasma Protein Binding (PPB):	23.813400268554688%
Volume Distribution (VD):	1.006
Pgp-substrate:	72.30552673339844%

ADMET: Metabolism

CYP1A2-inhibitor:	0.016
CYP1A2-substrate:	0.079
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.438
CYP2C9-inhibitor:	0.008
CYP2C9-substrate:	0.078
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.155
CYP3A4-inhibitor:	0.263
CYP3A4-substrate:	0.438

ADMET: Excretion

Clearance (CL):	2.868
Half-life (T1/2):	0.882

ADMET: Toxicity

hERG Blockers:	0.077
Human Hepatotoxicity (H-HT):	0.943
Drug-inuced Liver Injury (DILI):	0.828
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.382
Maximum Recommended Daily Dose:	0.12
Skin Sensitization:	0.128
Carcinogencity:	0.075
Eye Corrosion:	0.005
Eye Irritation:	0.022
Respiratory Toxicity:	0.066

Download Data

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

Natural Product: NPC79523

Natural Product ID:	NPC79523
*Common Name:**	BRHFNKAWPNHEJL-IFNHDBSHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BRHFNKAWPNHEJL-IFNHDBSHSA-N
Standard InCHI:	InChI=1S/C21H31NO8/c1-6-15-18(29-13(3)23)12(2)21(4,27)20(26)28-11-14-7-9-22(5)10-8-16(17(14)24)30-19(15)25/h7,12,15-16,18,27H,6,8-11H2,1-5H3/b14-7-/t12-,15+,16-,18-,21-/m1/s1
SMILES:	CC[C@H]1[C@@H]([C@@H](C)[C@](C)(C(=O)OCC2=CCN(C)CC[C@H](C2=O)OC1=O)O)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0001986] Tricarboxylic acids and derivatives

*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
NPO15949	Cystophora moniliformis	Species	Sargassaceae	Eukaryota	n.a.	southern Australian	n.a.	PMID[18687007]
NPO8369	Antiaris toxicaria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20553004]
NPO8369	Antiaris toxicaria	Species	Moraceae	Eukaryota	latex	Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan Province, China	2011-Mar	PMID[24033101]
NPO8369	Antiaris toxicaria	Species	Moraceae	Eukaryota	trunk bark	Yunnan, China	n.a.	PMID[24582402]
NPO5133	Annona spinescens	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8699188]
NPO5133	Annona spinescens	Species	Annonaceae	Eukaryota	seeds	n.a.	n.a.	PMID[9461649]
NPO8369	Antiaris toxicaria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11092	Asclepias eriocarpa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16502	Lepidium virginicum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8369	Antiaris toxicaria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16502	Lepidium virginicum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5133	Annona spinescens	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4259	Spiraea thunbergii	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11092	Asclepias eriocarpa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11092	Asclepias eriocarpa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5956	Polygonatum falcatum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11092	Asclepias eriocarpa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9629	Actinoplanes missouriensis	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO3257	Andryala ragusina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4259	Spiraea thunbergii	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5956	Polygonatum falcatum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5133	Annona spinescens	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15745	Gentiana asclepiadea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14353	Actinopyga mauritiana	Species	Holothuriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16502	Lepidium virginicum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15841	Clitoria macrophylla	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3548	Rheedia benthamiana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12941	Malus toringoides	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8369	Antiaris toxicaria	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2297	Parthenium integrifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15949	Cystophora moniliformis	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4404	Euodia merrillii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12112	Jurinea suffruticosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7369	Antennaria canadensis	Species	Carabidae	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 NPC79523 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	124
0.1-0.2	837
0.2-0.3	4004
0.3-0.4	13004
0.4-0.5	17036
0.5-0.6	6240
0.6-0.7	1365
0.7-0.8	80
0.8-0.85	0
0.85-0.9	0
0.9-0.95	7
0.95-1	0

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 NPC79523 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	105
0.1-0.2	870
0.2-0.3	3318
0.3-0.4	3328
0.4-0.5	1204
0.5-0.6	286
0.6-0.7	35
0.7-0.8	4
0.8-0.85	0
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