Structure

Physi-Chem Properties

Molecular Weight:  175.05
Volume:  160.471
LogP:  -1.361
LogD:  -0.912
LogS:  -2.464
# Rotatable Bonds:  0
TPSA:  112.08
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.434
Synthetic Accessibility Score:  3.605
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.515
MDCK Permeability:  4.954139512847178e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.624
Human Intestinal Absorption (HIA):  0.943
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.016

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.256
Plasma Protein Binding (PPB):  36.06513214111328%
Volume Distribution (VD):  0.478
Pgp-substrate:  65.59667205810547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.055
CYP1A2-substrate:  0.975
CYP2C19-inhibitor:  0.257
CYP2C19-substrate:  0.035
CYP2C9-inhibitor:  0.023
CYP2C9-substrate:  0.005
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.019
CYP3A4-inhibitor:  0.038
CYP3A4-substrate:  0.393

ADMET: Excretion

Clearance (CL):  5.572
Half-life (T1/2):  0.963

ADMET: Toxicity

hERG Blockers:  0.058
Human Hepatotoxicity (H-HT):  0.997
Drug-inuced Liver Injury (DILI):  0.986
AMES Toxicity:  0.895
Rat Oral Acute Toxicity:  0.99
Maximum Recommended Daily Dose:  0.284
Skin Sensitization:  0.753
Carcinogencity:  0.906
Eye Corrosion:  0.004
Eye Irritation:  0.917
Respiratory Toxicity:  0.982

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC327941

Natural Product ID:  NPC327941
Common Name*:   2-Amino-4-Oxo-1,7-Dihydropyrrolo[2,3-D]Pyrimidine-5-Carbonitrile
IUPAC Name:   2-amino-4-oxo-1,7-dihydropyrrolo[2,3-d]pyrimidine-5-carbonitrile
Synonyms:  
Standard InCHIKey:  FMKSMYDYKXQYRV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H5N5O/c8-1-3-2-10-5-4(3)6(13)12-7(9)11-5/h2H,(H4,9,10,11,12,13)
SMILES:  N#Cc1c[nH]c2c1c(O)nc(=N)[nH]2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL577120
PubChem CID:   446357
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001799] Pyrrolopyrimidines
        • [CHEMONTID:0004415] Pyrrolo[2,3-d]pyrimidines

*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
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1016/0006-291X(79)91731-5]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1093/emboj/18.8.2021]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1091286]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[10977898]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1100617]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11745165]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11750815]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12369847]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12467448]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12805358]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. ChEBI[131529]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13610867]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13831814]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[14973046]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15031653]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15292242]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15610037]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1644759]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[16630633]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[170247]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[17765195]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[179975]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19026742]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19514719]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19561621]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21437340]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21988831]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22289691]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22855027]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23537328]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23676670]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[241475]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24206068]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24783849]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24831709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24939187]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24966042]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24967680]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[2543976]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[25867074]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26195826]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26337258]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26670289]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26826371]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[29897754]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[30302998]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[318639]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[3283102]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[398096]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4877125]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4879561]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4908789]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[5332408]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6102982]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6284709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6338507]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7042909]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7601837]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[8852895]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[9470222]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria 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
NPT2621 Individual Protein Pteridine reductase 1 Leishmania major Ki > 27000.0 nM PMID[469467]
NPT2 Others Unspecified Ki = 5800.0 nM PMID[469467]

☑ 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 NPC327941 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
0.9077 High Similarity NPC314646
0.9008 High Similarity NPC62151
0.6627 Remote Similarity NPC222174
0.6545 Remote Similarity NPC33382
0.6533 Remote Similarity NPC194541
0.6446 Remote Similarity NPC41333
0.6287 Remote Similarity NPC162268
0.6048 Remote Similarity NPC212742
0.6048 Remote Similarity NPC475870
0.6012 Remote Similarity NPC89562
0.5987 Remote Similarity NPC306397
0.5977 Remote Similarity NPC313730
0.5976 Remote Similarity NPC131718
0.593 Remote Similarity NPC125659
0.593 Remote Similarity NPC168702
0.592 Remote Similarity NPC302647
0.5909 Remote Similarity NPC196580
0.5874 Remote Similarity NPC327613
0.5838 Remote Similarity NPC34300
0.5838 Remote Similarity NPC49217
0.5829 Remote Similarity NPC242209
0.5814 Remote Similarity NPC102423
0.5813 Remote Similarity NPC8590
0.581 Remote Similarity NPC314491
0.5802 Remote Similarity NPC197068
0.5797 Remote Similarity NPC59314
0.5783 Remote Similarity NPC282531
0.5779 Remote Similarity NPC212125
0.5769 Remote Similarity NPC321929
0.5742 Remote Similarity NPC57279
0.5695 Remote Similarity NPC15566
0.5677 Remote Similarity NPC165370
0.5618 Remote Similarity NPC313791
0.5616 Remote Similarity NPC63433
0.5603 Remote Similarity NPC163105
0.5602 Remote Similarity NPC159856

  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 NPC327941 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
0.6554 Remote Similarity NPD2127 Suspended
0.6316 Remote Similarity NPD2928 Phase 2
0.625 Remote Similarity NPD2134 Approved
0.625 Remote Similarity NPD2136 Approved
0.625 Remote Similarity NPD2135 Approved
0.618 Remote Similarity NPD706 Phase 1
0.6131 Remote Similarity NPD527 Clinical (unspecified phase)
0.6114 Remote Similarity NPD3916 Clinical (unspecified phase)
0.6114 Remote Similarity NPD3917 Approved
0.6114 Remote Similarity NPD3918 Approved
0.6062 Remote Similarity NPD3915 Approved
0.6033 Remote Similarity NPD4998 Phase 3
0.6033 Remote Similarity NPD4999 Phase 3
0.5987 Remote Similarity NPD9080 Approved
0.5969 Remote Similarity NPD4559 Clinical (unspecified phase)
0.5944 Remote Similarity NPD2814 Clinical (unspecified phase)
0.5928 Remote Similarity NPD3014 Clinical (unspecified phase)
0.5928 Remote Similarity NPD3013 Phase 3
0.5912 Remote Similarity NPD2872 Phase 2
0.5886 Remote Similarity NPD1599 Approved
0.5843 Remote Similarity NPD1046 Clinical (unspecified phase)
0.5838 Remote Similarity NPD1234 Discontinued
0.5797 Remote Similarity NPD8837 Clinical (unspecified phase)
0.5784 Remote Similarity NPD1286 Suspended
0.5779 Remote Similarity NPD9284 Approved
0.5773 Remote Similarity NPD796 Phase 2
0.5769 Remote Similarity NPD8827 Approved
0.5744 Remote Similarity NPD4612 Discontinued
0.5737 Remote Similarity NPD3814 Phase 1
0.573 Remote Similarity NPD1043 Phase 3
0.5724 Remote Similarity NPD515 Phase 1
0.5692 Remote Similarity NPD1197 Approved
0.5691 Remote Similarity NPD3593 Approved
0.5676 Remote Similarity NPD307 Approved
0.5652 Remote Similarity NPD1063 Phase 2
0.5611 Remote Similarity NPD2293 Phase 2
0.5608 Remote Similarity NPD9360 Approved

  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