Structure of PDB 4gmd Chain D Binding Site BS01

Receptor Information
>4gmd Chain D (length=196) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGLFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTREPGGTPLAERIRE
LLLAPSDEPMAADTELLLMFAARAQHLAGVIRPALARGAVVLCDRFTDAT
YAYQGGGRGLPEARIAALESFVQGDLRPDLTLVFDLPVLDRFEQEDRRFF
EAVRQTYLQRAAQAPERYQVLDAGLPLAEVQAGLDRLLPNLLERLN
Ligand information
Ligand IDATM
InChIInChI=1S/C10H14N5O7P/c1-5-3-15(10(17)12-9(5)16)8-2-6(13-14-11)7(22-8)4-21-23(18,19)20/h3,6-8H,2,4H2,1H3,(H,12,16,17)(H2,18,19,20)/t6-,7+,8+/m0/s1
InChIKeyOIFWQOKDSPDILA-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](N=[N+]=[N-])[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(\N=[N+]=[N-])C2)COP(=O)(O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)N=[N+]=[N-]
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)N=[N+]=[N-]
CACTVS 3.341CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H14 N5 O7 P
Name3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL257695
DrugBankDB03666
ZINCZINC000012503817
PDB chain4gmd Chain D Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4gmd The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with AZT Monophosphate
Resolution1.98 Å
Binding residue
(original residue number in PDB)		E39 P40 R50 M70 R74 R96 A100 T101 Y104 Q105 D153 F155
Binding residue
(residue number reindexed from 1)		E38 P39 R49 M69 R73 R95 A99 T100 Y103 Q104 D140 F142
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.4.9: dTMP kinase.
Gene Ontology
Molecular Function
GO:0004798 thymidylate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
Biological Process
GO:0006227 dUDP biosynthetic process
GO:0006233 dTDP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0016310 phosphorylation
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4gmd, PDBe:4gmd, PDBj:4gmd
PDBsum4gmd
PubMed
UniProtQ9HZN8|KTHY_PSEAE Thymidylate kinase (Gene Name=tmk)

[Back to BioLiP]