NPASS Compound

Structure

NPC220647 OpenBabel06302216212D 29 31 0 0 0 0 0 0 0 0999 V2000 7.5777 -9.2322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4913 -8.8255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5958 -7.8310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7868 -7.2432 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8913 -6.2487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0823 -5.6609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1868 -4.6664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3778 -4.0786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4824 -3.0841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6733 -2.4963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7779 -1.5018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9688 -0.9140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0178 -1.2230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4300 -0.4140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0178 0.3950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9688 0.0860 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.7088 1.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7306 1.5540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3239 2.4676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3294 2.3630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1215 1.3849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9875 0.8849 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.2079 0.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6581 1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9945 -0.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.8239 3.3336 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3239 4.1996 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 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 16 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 17 18 2 0 0 0 0 18 22 1 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 28 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 27 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	393.28
Volume:	438.612
LogP:	7.771
LogD:	5.303
LogS:	-4.91
# Rotatable Bonds:	12
TPSA:	56.6
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.35
Synthetic Accessibility Score:	3.37
Fsp3:	0.44
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.405
MDCK Permeability:	1.3668121027876623e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.182
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.533
30% Bioavailability (F30%):	0.157

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.094
Plasma Protein Binding (PPB):	98.79895782470703%
Volume Distribution (VD):	4.474
Pgp-substrate:	1.131630778312683%

ADMET: Metabolism

CYP1A2-inhibitor:	0.863
CYP1A2-substrate:	0.823
CYP2C19-inhibitor:	0.833
CYP2C19-substrate:	0.069
CYP2C9-inhibitor:	0.706
CYP2C9-substrate:	0.981
CYP2D6-inhibitor:	0.782
CYP2D6-substrate:	0.896
CYP3A4-inhibitor:	0.899
CYP3A4-substrate:	0.152

ADMET: Excretion

Clearance (CL):	4.343
Half-life (T1/2):	0.228

ADMET: Toxicity

hERG Blockers:	0.86
Human Hepatotoxicity (H-HT):	0.769
Drug-inuced Liver Injury (DILI):	0.276
AMES Toxicity:	0.019
Rat Oral Acute Toxicity:	0.771
Maximum Recommended Daily Dose:	0.965
Skin Sensitization:	0.959
Carcinogencity:	0.062
Eye Corrosion:	0.011
Eye Irritation:	0.611
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC220647

Natural Product ID:	NPC220647
*Common Name:**	undecylprodigiosin
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HIYSWASSDOXZLC-MOHJPFBDSA-N
Standard InCHI:	InChI=1S/C25H35N3O/c1-3-4-5-6-7-8-9-10-11-13-20-15-16-21(27-20)18-24-25(29-2)19-23(28-24)22-14-12-17-26-22/h12,14-19,26-27H,3-11,13H2,1-2H3/b24-18-
SMILES:	CCCCCCCCCCCC1=CC=C(N1)/C=C2/C(=CC(=N2)C3=CC=CN3)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	135515151
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000090] Pyrroles [CHEMONTID:0002257] Substituted pyrroles [CHEMONTID:0002028] Dipyrrins

*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
NPO41497	Streptomyces coelicolor A3 (2) + Escherichia coli C600	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	DOI[10.1016/j.bej.2010.11.008]
NPO41496	Streptomyces coelicolor A3 (2) + Bacillus subtilis ATCC 6633	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[20878541]
NPO41505	Streptomyces lividans TK23 + One of mycolic acid-containing bacteria	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[21097597]
NPO41504	Streptomyces lividans 66 + Verticillium dahliae	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[22151498]
NPO41498	Streptomyces coelicolor M145 + Corallococcus coralloides B035	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[24249103]
NPO41493	Streptomyces coelicolor + Corallococcus coralloides	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[24249103]
NPO41494	Streptomyces Coelicolor + Escherichia coli	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[27241291]
NPO41497	Streptomyces coelicolor A3 (2) + Escherichia coli C600	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[27241291]

☑ 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 NPC220647 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC220647 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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