Structure of PDB 1h79 Chain A Binding Site BS03

Receptor Information
>1h79 Chain A (length=559) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRVFPTQRDLMAGIVSKHIAKNMVPSFIMKAHESGIIHVHDIDYSPALPF
TNCCLVDLKGMLENGFKLGNAQIETPKSIGVATAIMAQITAQVASHQYGG
TTFANVDKVLSPYVKRTYAKHIEDAEKWQIADALNYAQSKTEKDVYDAFQ
AYEYEVNTLFSSNGQTPFVTITFGTGTDWTERMIQKAILKNRIKGLGRDG
ITPIFPKLVMFVEEGVNLYKDDPNYDIKQLALECASKRMYPDIISAKNNK
AITGSSVPVSPMGCRSFLSVWKDSTGNEILDGRNNLGVVTLNLPRIALDS
YIGTQFNEQKFVELFNERMDLCFEALMCRISSLKGVKATVAPILYQEGAF
GVRLKPDDDIIELFKNGRSSVSLGYIGIHELNILVGRDIGREILTKMNAH
LKQWTERTGFAFSLYSTPAENLCYRFCKLDTEKYGSVKDVTDKGWYTNSF
HVSVEENITPFEKISREAPYHFIATGGHISYVELPDMKNNLKGLEAVWDY
AAQHLDYFGVNMPVDKCFTCGSTHEMTPTENGFVCSICGETDPKKMNTIR
RTCAYLGNP
Ligand information
Ligand IDTTP
InChIInChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyNHVNXKFIZYSCEB-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O14 P3
NameTHYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL363559
DrugBankDB02452
ZINCZINC000008215959
PDB chain1h79 Chain A Residue 1589 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1h79 Structural Basis for Allosteric Substrate Specificty Regulation in Anaerobic Ribonucleotide Reductase
Resolution2.9 Å
Binding residue
(original residue number in PDB)		H64 H66 Q191 A445 E446 N447 L448 R451
Binding residue
(residue number reindexed from 1)		H38 H40 Q165 A419 E420 N421 L422 R425
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.89,Kd=13uM
Enzymatic activity
Catalytic site (original residue number in PDB) N78 C79 M288 C290 S292 N311 Y441 E446 A580
Catalytic site (residue number reindexed from 1) N52 C53 M262 C264 S266 N285 Y415 E420 A554
Enzyme Commision number 1.1.98.6: ribonucleoside-triphosphate reductase (formate).
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0008998 ribonucleoside-triphosphate reductase (thioredoxin) activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0009265 2'-deoxyribonucleotide biosynthetic process
Cellular Component
GO:0031250 anaerobic ribonucleoside-triphosphate reductase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1h79, PDBe:1h79, PDBj:1h79
PDBsum1h79
PubMed11587648
UniProtP07071|NRDD_BPT4 Anaerobic ribonucleoside-triphosphate reductase (Gene Name=nrdD)

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