NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	268.12
Volume:	244.381
LogP:	-1.557
LogD:	-0.771
LogS:	-1.232
# Rotatable Bonds:	2
TPSA:	112.13
# H-Bond Aceptor:	8
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.537
Synthetic Accessibility Score:	4.72
Fsp3:	0.636
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.381
MDCK Permeability:	6.024963568052044e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.35
20% Bioavailability (F20%):	0.988
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.406
Plasma Protein Binding (PPB):	13.603092193603516%
Volume Distribution (VD):	1.638
Pgp-substrate:	86.97960662841797%

ADMET: Metabolism

CYP1A2-inhibitor:	0.018
CYP1A2-substrate:	0.047
CYP2C19-inhibitor:	0.022
CYP2C19-substrate:	0.431
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.488
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.174
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.095

ADMET: Excretion

Clearance (CL):	2.556
Half-life (T1/2):	0.467

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.913
Drug-inuced Liver Injury (DILI):	0.965
AMES Toxicity:	0.943
Rat Oral Acute Toxicity:	0.088
Maximum Recommended Daily Dose:	0.967
Skin Sensitization:	0.111
Carcinogencity:	0.906
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.487

Download Data

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

Natural Product: NPC74306

Natural Product ID:	NPC74306
*Common Name:**	Pentostatin
IUPAC Name:	(8R)-3-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-7,8-dihydro-4H-imidazo[4,5-d][1,3]diazepin-8-ol
Synonyms:	CI-825; Nipent; PD-81565; Pentostatin
Standard InCHIKey:	FPVKHBSQESCIEP-JQCXWYLXSA-N
Standard InCHI:	InChI=1S/C11H16N4O4/c16-3-8-6(17)1-9(19-8)15-5-14-10-7(18)2-12-4-13-11(10)15/h4-9,16-18H,1-3H2,(H,12,13)/t6-,7+,8+,9+/m0/s1
SMILES:	C1[C@@H]([C@@H](CO)O[C@H]1n1cnc2[C@@H](CN=CNc12)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1580
PubChem CID:	439693
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001979] Imidazodiazepines

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7264680]
NPO17888	Myxococcus xanthus	Species	Myxococcaceae	Bacteria	n.a.	n.a.	n.a.	PMID[31465225]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28581744]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	Stem Bark	n.a.	n.a.	PMID[28240909]
NPO24105	Artemisia iwayomogi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23510022]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	Northeastern Regional Plant Introduction Station at Geneva	1966, 1967, and 1968 crop seasons	PMID[18460139]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	needles	Himalayan	n.a.	PMID[16480866]
NPO22210	Allium ampeloprasum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15877880]
NPO17888	Myxococcus xanthus	Species	Myxococcaceae	Bacteria	n.a.	n.a.	n.a.	PMID[14575429]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

Activity Type	# Activity
AC50	3
IC50	5
Ki	12
Others	61
Potency	1

Activity Type	# Activity
Cell Line	2
Individual Protein	12
NON-MOLECULAR	5
Organism	16
Others	17
PHENOTYPE	26
SINGLE PROTEIN	4

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	""	Potency	n.a.	33491.5	nM	PubChem BioAssay data set
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	20000.0	nM	PMID[546016]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	19952.62	nM	PMID[546016]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-0.07	%	PMID[546015]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-0.02	%	PMID[546014]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	13.02	%	PMID[546013]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	10.69	%	PMID[546012]
NPT3838	Individual Protein	Adenosine deaminase	Homo sapiens	Ki	=	0.5	nM	PMID[546011]
NPT3838	Individual Protein	Adenosine deaminase	Homo sapiens	Ki	=	0.026	nM	PMID[546011]
NPT27704	SINGLE PROTEIN	Adenosine deaminase	Plasmodium falciparum	Ki	=	8.2	nM	PMID[546011]

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☑ 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 NPC74306 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	567
0.1-0.2	27231
0.2-0.3	9582
0.3-0.4	4342
0.4-0.5	679
0.5-0.6	148
0.6-0.7	87
0.7-0.8	57
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC315642
0.8741	High Similarity	NPC262926
0.8676	High Similarity	NPC61198
0.8456	Intermediate Similarity	NPC324009
0.8417	Intermediate Similarity	NPC30326

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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 NPC74306 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	152
0.1-0.2	1876
0.2-0.3	3452
0.3-0.4	2449
0.4-0.5	892
0.5-0.6	194
0.6-0.7	101
0.7-0.8	32
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD582	Approved
0.8864	High Similarity	NPD9632	Phase 3
0.8676	High Similarity	NPD252	Clinical (unspecified phase)
0.8467	Intermediate Similarity	NPD194	Clinical (unspecified phase)
0.8298	Intermediate Similarity	NPD549	Approved

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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