NPASS Compound

Structure

NPC56133 OpenBabel06302215342D 29 32 0 0 1 0 0 0 0 0999 V2000 0.4056 3.6496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5890 3.7541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1767 2.9451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7700 2.0316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3578 1.2226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3523 1.3271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9401 0.5181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5334 -0.3955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5388 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9511 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7071 0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4483 1.6730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1554 2.3801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1213 2.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3801 1.1554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6730 0.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3461 0.8966 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8284 2.8284 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2588 -1.9659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9659 -1.2588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1211 -1.2045 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7591 2.2406 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1713 3.0497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9957 4.6677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 29 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 13 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 27 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 26 1 0 0 0 0 9 13 1 0 0 0 0 9 10 1 0 0 0 0 11 10 1 1 0 0 0 11 12 1 0 0 0 0 11 23 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 1 6 0 0 0 14 23 1 0 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 19 2 0 0 0 0 18 22 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 27 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	394.21
Volume:	423.436
LogP:	6.569
LogD:	4.381
LogS:	-2.814
# Rotatable Bonds:	4
TPSA:	69.92
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.48
Synthetic Accessibility Score:	4.075
Fsp3:	0.44
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.891
MDCK Permeability:	1.6694128134986386e-05
Pgp-inhibitor:	0.864
Pgp-substrate:	0.863
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.985
30% Bioavailability (F30%):	0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.012
Plasma Protein Binding (PPB):	96.52684783935547%
Volume Distribution (VD):	3.06
Pgp-substrate:	2.9232139587402344%

ADMET: Metabolism

CYP1A2-inhibitor:	0.318
CYP1A2-substrate:	0.847
CYP2C19-inhibitor:	0.803
CYP2C19-substrate:	0.153
CYP2C9-inhibitor:	0.743
CYP2C9-substrate:	0.954
CYP2D6-inhibitor:	0.741
CYP2D6-substrate:	0.729
CYP3A4-inhibitor:	0.248
CYP3A4-substrate:	0.423

ADMET: Excretion

Clearance (CL):	16.268
Half-life (T1/2):	0.351

ADMET: Toxicity

hERG Blockers:	0.027
Human Hepatotoxicity (H-HT):	0.29
Drug-inuced Liver Injury (DILI):	0.083
AMES Toxicity:	0.019
Rat Oral Acute Toxicity:	0.623
Maximum Recommended Daily Dose:	0.941
Skin Sensitization:	0.947
Carcinogencity:	0.043
Eye Corrosion:	0.003
Eye Irritation:	0.816
Respiratory Toxicity:	0.924

Download Data

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

Natural Product: NPC56133

Natural Product ID:	NPC56133
*Common Name:**	GZFNBAIGMIFCNM-DPSWKAHMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GZFNBAIGMIFCNM-DPSWKAHMSA-N
Standard InCHI:	InChI=1S/C25H30O4/c1-13(2)6-8-15-21(29-5)12-19(27)16-11-17-23(22(15)16)24(25(17,3)4)14-7-9-18(26)20(28)10-14/h6-7,9-10,12,17,23-24,26-28H,8,11H2,1-5H3/t17-,23-,24-/m0/s1
SMILES:	CC(=CCc1c(cc(c2C[C@H]3[C@@H](c12)[C@H](c1ccc(c(c1)O)O)C3(C)C)O)OC)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	16080288
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000027] Indanes

*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
NPO28803	Artocarpus chama	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[15165133]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29318	Cereus validus	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29386	Agabus bipustulatus	Species	Dytiscidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28969	Solanum sarrachoides	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29519	Primula glaucescens	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29462	Helinus ovatus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28803	Artocarpus chama	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29358	Senecio oxyodon	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29409	Oenothera laciniata	Species	Onagraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29156	Conyza incana	Species	Asteraceae	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 NPC56133 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	477
0.1-0.2	1761
0.2-0.3	4215
0.3-0.4	12466
0.4-0.5	6222
0.5-0.6	4647
0.6-0.7	8945
0.7-0.8	3253
0.8-0.85	575
0.85-0.9	135
0.9-0.95	1
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 NPC56133 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	396
0.1-0.2	979
0.2-0.3	1764
0.3-0.4	2868
0.4-0.5	1632
0.5-0.6	938
0.6-0.7	513
0.7-0.8	56
0.8-0.85	4
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