NPASS Compound

Structure

NPC192436 OpenBabel06302215432D 45 49 0 0 1 0 0 0 0 0999 V2000 0.9157 -0.2975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7493 -0.7788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7491 -1.7414 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5828 -2.2227 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4166 -1.7414 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4164 -0.7788 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2500 -1.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2500 -0.2975 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0836 -0.7788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9630 -0.3873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6070 -1.1026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1258 -1.9362 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1842 -1.7361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2500 0.6651 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4164 1.1464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4164 2.1089 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5828 0.6651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5828 -0.2975 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7494 0.1836 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9157 -0.2975 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9156 0.6651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9157 -1.2603 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9158 -2.2229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0001 -1.5578 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2973 -2.4733 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2388 -2.6735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8829 -1.9582 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5362 -3.5889 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4778 -3.7891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3468 -3.1886 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0494 -4.1041 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8921 -4.3042 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6935 -4.8193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5659 -0.7789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3995 -0.2977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3995 -1.2603 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 4.2502 -2.2226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0502 -3.1641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7655 -3.8081 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1347 -3.4616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5827 -3.1853 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9386 -3.9007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2360 -4.8161 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9971 -3.7005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 18 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 22 1 0 0 0 0 4 5 1 0 0 0 0 4 42 1 6 0 0 0 5 6 1 0 0 0 0 5 38 1 1 0 0 0 6 18 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 1 0 0 0 8 14 1 0 0 0 0 9 13 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 18 17 1 1 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 37 1 0 0 0 0 20 21 1 1 0 0 0 20 22 1 0 0 0 0 22 23 1 1 0 0 0 22 24 1 0 0 0 0 24 25 1 1 0 0 0 24 34 1 0 0 0 0 25 26 1 6 0 0 0 25 30 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 34 35 1 0 0 0 0 34 36 1 0 0 0 0 34 37 1 0 0 0 0 38 39 1 0 0 0 0 39 40 2 0 0 0 0 39 41 1 0 0 0 0 42 43 1 0 0 0 0 43 44 2 0 0 0 0 43 45 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	632.25
Volume:	612.427
LogP:	2.752
LogD:	1.263
LogS:	-4.725
# Rotatable Bonds:	10
TPSA:	163.1
# H-Bond Aceptor:	13
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.255
Synthetic Accessibility Score:	6.833
Fsp3:	0.656
Lipinski Rule-of-5:	Rejected
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:	-5.337
MDCK Permeability:	9.063857578439638e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.019
Human Intestinal Absorption (HIA):	0.726
20% Bioavailability (F20%):	0.954
30% Bioavailability (F30%):	0.961

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.229
Plasma Protein Binding (PPB):	56.518157958984375%
Volume Distribution (VD):	1.468
Pgp-substrate:	34.908931732177734%

ADMET: Metabolism

CYP1A2-inhibitor:	0.009
CYP1A2-substrate:	0.05
CYP2C19-inhibitor:	0.065
CYP2C19-substrate:	0.118
CYP2C9-inhibitor:	0.101
CYP2C9-substrate:	0.004
CYP2D6-inhibitor:	0.089
CYP2D6-substrate:	0.063
CYP3A4-inhibitor:	0.76
CYP3A4-substrate:	0.663

ADMET: Excretion

Clearance (CL):	5.749
Half-life (T1/2):	0.705

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.912
Drug-inuced Liver Injury (DILI):	0.959
AMES Toxicity:	0.533
Rat Oral Acute Toxicity:	0.979
Maximum Recommended Daily Dose:	0.539
Skin Sensitization:	0.118
Carcinogencity:	0.364
Eye Corrosion:	0.003
Eye Irritation:	0.022
Respiratory Toxicity:	0.968

Download Data

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

Natural Product: NPC192436

Natural Product ID:	NPC192436
*Common Name:**	JBHDNDUBXWNGRJ-LCJPWZFKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JBHDNDUBXWNGRJ-LCJPWZFKSA-N
Standard InCHI:	InChI=1S/C32H40O13/c1-15-21-22(40-16(2)33)26(42-18(4)35)30(8)25(19-11-12-39-14-19)43-20(36)13-32(15,30)45-31(9)29(21,7)24(28(5,6)44-31)23(27(37)38-10)41-17(3)34/h11-12,14,21-26H,1,13H2,2-10H3/t21-,22-,23+,24+,25+,26+,29-,30-,31-,32+/m1/s1
SMILES:	C=C1[C@@H]2[C@H]([C@@H]([C@@]3(C)[C@H](c4ccoc4)OC(=O)C[C@]13O[C@]1(C)[C@@]2(C)[C@@H]([C@@H](C(=O)OC)OC(=O)C)C(C)(C)O1)OC(=O)C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102156440
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0002995] Pentacarboxylic 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
NPO12306	Gonospermum canariense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12880311]
NPO17039	Pharbitis nil	Species	Convolvulaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[19435339]
NPO26904	Salvia hypargeia	Species	Lamiaceae	Eukaryota	roots	n.a.	n.a.	PMID[3236010]
NPO17039	Pharbitis nil	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17039	Pharbitis nil	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17039	Pharbitis nil	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26904	Salvia hypargeia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24539	Veronica cupressoides	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12306	Gonospermum canariense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12277	Dendroctonus pseudotsugae	Species	Curculionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26137	Aplidium conicum	Species	Polyclinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26082	Flindersia laevicarpa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25795	Neurolaena macrophylla	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26784	Olea capensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26609	Nauclea gambir	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26928	Zanthoxylum capense	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26861	Epinetrum cordifolium	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO26729	Aster indicus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26167	Strychnos cocculoides	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26974	Morella cerifera	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26728	Calycanthus chinensis	Species	Calycanthaceae	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 NPC192436 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	428
0.1-0.2	1550
0.2-0.3	3383
0.3-0.4	6006
0.4-0.5	10497
0.5-0.6	9738
0.6-0.7	9015
0.7-0.8	1632
0.8-0.85	260
0.85-0.9	164
0.9-0.95	24
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 NPC192436 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	358
0.1-0.2	999
0.2-0.3	2291
0.3-0.4	2724
0.4-0.5	1787
0.5-0.6	723
0.6-0.7	246
0.7-0.8	20
0.8-0.85	2
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