Structure of PDB 6vdd Chain D Binding Site BS03

Receptor Information
>6vdd Chain D (length=567) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRALEPGELAAWLSEHSLGSRFGVAVVGTHKAYDADATALAIVAADGDGR
YIDTSTLTPEDEAALASWLADPGPPKALHEAKLAMHDLAGRGWTLRGVTS
DTALAAYLVRPGQRSFTLDDLAVRYLHRELRQAVQTVILRACAVLDLADA
LDQELARIDSLSLLSRMELPVQRTLAEMEHAGIAVDLGMLEQLQSEFADQ
IRDAAEAAYSVIGKQINLGSPKQLQAVLFDELEMPKTKKTKTGYTTDADA
LQSLFEKTGHPFLQHLLAHRDATRLKVTVDGLLNSVASDGRIHTTFNQTI
AATGRLSSTEPNLQNIPIRTEAGRRIRDAFVVGEGYAELMTADYSQIEMR
IMAHLSRDAGLIEAFNTGEDLHSFVASRAFSVPIDEVTPELRRRVKAMSY
GLAYGLSAYGLAQQLKISTEEAKVQMEQYFDRFGGVRDYLRDVVDQARKD
GYTSTVLGRRRYLPELDSSNRQVREAAERAALNAPIQGSAADIIKVAMIN
VDQAIKDAGLRSRILLQVHDELLFEVSEGEQGELEQLVREHMGNAYPLDV
PLEVSVGYGRSWDAAAH
Ligand information
Ligand IDDCT
InChIInChI=1S/C9H16N3O12P3/c10-7-3-4-12(9(13)11-7)8-2-1-6(22-8)5-21-26(17,18)24-27(19,20)23-25(14,15)16/h3-4,6,8H,1-2,5H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1
InChIKeyARLKCWCREKRROD-POYBYMJQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1CC(OC1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
OpenEye OEToolkits 1.5.0C1C[C@@H](O[C@@H]1CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@H]2CC[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2
FormulaC9 H16 N3 O12 P3
Name2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL1201384
DrugBank
ZINCZINC000013516800
PDB chain6vdd Chain D Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vdd Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Q687 H713 R733 K737 Y741
Binding residue
(residue number reindexed from 1)		Q346 H372 R392 K396 Y400
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0008408 3'-5' exonuclease activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6vdd, PDBe:6vdd, PDBj:6vdd
PDBsum6vdd
PubMed32034423
UniProtA0QYZ2

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