Structure of PDB 4f5p Chain A Binding Site BS05

Receptor Information
>4f5p Chain A (length=326) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSG
AEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGI
GPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEML
QMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRL
IPKDQYYCGVLYFTGSDIFNKNMKAHALEKGFTINEYTIRPLGVTGVAGE
PLPVDSEKDIFDYIQWKYREPKDRSE
Ligand information
Ligand IDF2A
InChIInChI=1S/C11H18N5O11P3/c12-10-9-11(14-3-13-10)16(4-15-9)8-1-6(17)7(26-8)2-25-28(18,19)5-29(20,21)27-30(22,23)24/h3-4,6-8,17H,1-2,5H2,(H,18,19)(H,20,21)(H2,12,13,14)(H2,22,23,24)/t6-,7+,8+/m0/s1
InChIKeyXETARULVTCYJAN-XLPZGREQSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)O3
FormulaC11 H18 N5 O11 P3
Name2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine
ChEMBLCHEMBL1162297
DrugBank
ZINC
PDB chain4f5p Chain A Residue 404 [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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PDB4f5p Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		S180 S188 G189 D190 D192 D276
Binding residue
(residue number reindexed from 1)		S174 S182 G183 D184 D186 D267
Annotation score1
Binding affinityBindingDB: Ki=5000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D190 D192 D256
Catalytic site (residue number reindexed from 1) D184 D186 D247
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
4.2.99.-
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0016779 nucleotidyltransferase activity
GO:0016829 lyase activity
GO:0019899 enzyme binding
GO:0034061 DNA polymerase activity
GO:0046872 metal ion binding
GO:0051575 5'-deoxyribose-5-phosphate lyase activity
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological Process
GO:0001701 in utero embryonic development
GO:0006259 DNA metabolic process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006287 base-excision repair, gap-filling
GO:0006290 pyrimidine dimer repair
GO:0006297 nucleotide-excision repair, DNA gap filling
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006915 apoptotic process
GO:0006954 inflammatory response
GO:0006974 DNA damage response
GO:0007435 salivary gland morphogenesis
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010332 response to gamma radiation
GO:0016445 somatic diversification of immunoglobulins
GO:0016446 somatic hypermutation of immunoglobulin genes
GO:0045471 response to ethanol
GO:0048535 lymph node development
GO:0048536 spleen development
GO:0048872 homeostasis of number of cells
GO:0051402 neuron apoptotic process
GO:0055093 response to hyperoxia
GO:0071707 immunoglobulin heavy chain V-D-J recombination
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005874 microtubule
GO:0005876 spindle microtubule
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4f5p, PDBe:4f5p, PDBj:4f5p
PDBsum4f5p
PubMed22959623
UniProtP06746|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)

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