NPASS Compound

Structure

NPC311113 OpenBabel06302216112D 43 47 0 0 1 0 0 0 0 0999 V2000 9.0726 2.5575 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5816 1.7062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5987 1.7057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1076 0.8543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1248 0.8539 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6337 0.0025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6509 0.0021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1598 -0.8493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1769 -0.8497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6851 0.0013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1762 0.8527 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7023 0.0009 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8509 0.4919 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8506 1.4753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0006 1.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8515 1.4748 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8518 2.4581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7032 1.9662 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7035 2.9490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5553 3.4404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4068 2.9485 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4071 3.9526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2586 3.4399 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1089 2.9480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1086 1.9652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4065 1.9657 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4062 0.9615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5547 1.4743 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5545 0.4909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7027 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8512 0.4914 0.0000 C 0 0 1 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 0.0003 -1.0042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8694 -0.5026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2591 4.4222 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2984 4.6270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9169 5.1519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6139 6.0863 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6531 6.2911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9954 5.5615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3501 7.2256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3894 7.4304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0079 7.9552 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 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 32 1 0 0 0 0 14 15 1 0 0 0 0 16 15 1 1 0 0 0 16 31 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 17 1 6 0 0 0 18 28 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 26 1 0 0 0 0 21 22 1 6 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 23 35 1 6 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 1 0 0 0 26 28 1 0 0 0 0 28 29 1 1 0 0 0 29 30 1 0 0 0 0 31 30 1 6 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 32 34 1 0 0 0 0 35 36 1 1 0 0 0 35 37 1 0 0 0 0 37 38 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 41 42 1 0 0 0 0 41 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	590.51
Volume:	681.944
LogP:	10.63
LogD:	7.138
LogS:	-7.772
# Rotatable Bonds:	13
TPSA:	26.3
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.074
Synthetic Accessibility Score:	5.728
Fsp3:	0.829
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
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:	-5.001
MDCK Permeability:	1.4496956282528117e-05
Pgp-inhibitor:	0.292
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.967
30% Bioavailability (F30%):	0.901

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.031
Plasma Protein Binding (PPB):	98.48526000976562%
Volume Distribution (VD):	1.387
Pgp-substrate:	1.643244981765747%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.199
CYP2C19-inhibitor:	0.12
CYP2C19-substrate:	0.968
CYP2C9-inhibitor:	0.084
CYP2C9-substrate:	0.482
CYP2D6-inhibitor:	0.511
CYP2D6-substrate:	0.623
CYP3A4-inhibitor:	0.835
CYP3A4-substrate:	0.852

ADMET: Excretion

Clearance (CL):	4.978
Half-life (T1/2):	0.012

ADMET: Toxicity

hERG Blockers:	0.909
Human Hepatotoxicity (H-HT):	0.192
Drug-inuced Liver Injury (DILI):	0.103
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.148
Maximum Recommended Daily Dose:	0.941
Skin Sensitization:	0.975
Carcinogencity:	0.058
Eye Corrosion:	0.408
Eye Irritation:	0.312
Respiratory Toxicity:	0.894

Download Data

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

Natural Product: NPC311113

Natural Product ID:	NPC311113
*Common Name:**	KJCDIXARAHBDPC-WCGUHVHZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KJCDIXARAHBDPC-WCGUHVHZSA-N
Standard InCHI:	InChI=1S/C41H66O2/c1-10-11-12-13-14-15-16-17-36(42)43-35-23-25-40-28-41(40)27-26-38(8)32(31(5)19-18-30(4)29(2)3)22-24-39(38,9)34(41)21-20-33(40)37(35,6)7/h14-17,29,31-35H,4,10-13,18-28H2,1-3,5-9H3/b15-14+,17-16+/t31-,32-,33+,34+,35+,38-,39+,40-,41+/m1/s1
SMILES:	CCCCC/C=C/C=C/C(=O)O[C@H]1CC[C@@]23C[C@@]43CC[C@]3(C)[C@H](CC[C@@]3(C)[C@@H]4CC[C@H]2C1(C)C)[C@H](C)CCC(=C)C(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44233424
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002321] Cycloartanols 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
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1021/np0201523]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12193012]
NPO26661	Heimia salicifolia	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3783154]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26172	Dryopteris sacrosancta	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26568	Rubus koehneanus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25876	Chromodoris inornata	Species	Chromodorididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29041	Scutellaria orientalis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26433	Conus marmoreus	Species	Conidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26383	Lemna trisulca	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26888	Narcissus asturiensis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26629	Caesalpinia pulcherrima	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4283	Tripteris vaillantii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26172	Dryopteris sacrosancta	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26190	Aspergillus wentii	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26215	Eleusine indica	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21665.1	Mycobacterium avium subsp. paratuberculosis	Subspecies	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO26906	Astragalus interpositus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26839	Microlepia speluncae	Species	Dennstaedtiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26931	Dolichothele uberiformis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO21295	Botryotrichum piluliferum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26411	Stemphylium radicinum	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26661	Heimia salicifolia	Species	Lythraceae	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 NPC311113 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	226
0.1-0.2	1329
0.2-0.3	4806
0.3-0.4	14601
0.4-0.5	8796
0.5-0.6	7156
0.6-0.7	4847
0.7-0.8	891
0.8-0.85	36
0.85-0.9	9
0.9-0.95	0
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 NPC311113 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	195
0.1-0.2	1329
0.2-0.3	4026
0.3-0.4	2542
0.4-0.5	635
0.5-0.6	194
0.6-0.7	208
0.7-0.8	21
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