Structure of PDB 4q5v Chain E Binding Site BS03

Receptor Information
>4q5v Chain E (length=865) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTL
YFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEK
NYAFEIPDVPEKSEYLEVKYSAEMPQLPQDLKGETFSHVFGTNTSSLELF
LMNRKIKGPCWLEVKSPQLLNQPVSWCKAEAMALKPDLVNVIKDVSPPPL
VVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVS
KPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGH
NIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGFGERNATCGRMIC
DVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYL
LEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFL
LLHAFYENNYIVPDKQIRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYP
SIIQEFNICFTTVQRVEQIPELPDPSLEMGILPREIRKLVERRKQVKQLM
KQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYK
GREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEV
NKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDI
VRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVP
VSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVI
CQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDG
IDAVLIATWLGLDPT
Ligand information
Ligand ID2ZE
InChIInChI=1S/C20H34O4/c1-17(11-21)15-4-3-13-9-14-10-19(13,7-8-20(14,24)12-22)18(15,2)6-5-16(17)23/h13-16,21-24H,3-12H2,1-2H3/t13-,14+,15-,16+,17-,18-,19-,20-/m0/s1
InChIKeyNOFOAYPPHIUXJR-APNQCZIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C[C@]12CC[C@H]([C@@]([C@@H]1CC[C@@H]3[C@@]24CC[C@@]([C@H](C3)C4)(CO)O)(C)CO)O
CACTVS 3.385C[C]1(CO)[CH](O)CC[C]2(C)[CH]1CC[CH]3C[CH]4C[C]23CC[C]4(O)CO
CACTVS 3.385C[C@@]1(CO)[C@H](O)CC[C@@]2(C)[C@H]1CC[C@H]3C[C@@H]4C[C@]23CC[C@]4(O)CO
ACDLabs 12.01OCC4(O)C3CC2C(C1(C(C(C)(CO)C(O)CC1)CC2)C)(C3)CC4
OpenEye OEToolkits 1.7.6CC12CCC(C(C1CCC3C24CCC(C(C3)C4)(CO)O)(C)CO)O
FormulaC20 H34 O4
Name(3R,4R,4aR,6aS,8R,9R,11aS,11bS)-4,9-bis(hydroxymethyl)-4,11b-dimethyltetradecahydro-8,11a-methanocyclohepta[a]naphthale ne-3,9-diol;
Aphidicolin
ChEMBLCHEMBL29711
DrugBankDB17742
ZINCZINC000003789195
PDB chain4q5v Chain E Residue 1301 [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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PDB4q5v Structural basis for inhibition of DNA replication by aphidicolin.
Resolution2.52 Å
Binding residue
(original residue number in PDB)
L864 Y865 N954 S955 Y957 G958
Binding residue
(residue number reindexed from 1)
L498 Y499 N575 S576 Y578 G579
Annotation score1
Binding affinityBindingDB: IC50=4300nM,EC50=2000nM
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:1902975 mitotic DNA replication initiation

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Molecular Function

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Biological Process
External links
PDB RCSB:4q5v, PDBe:4q5v, PDBj:4q5v
PDBsum4q5v
PubMed25429975
UniProtP09884|DPOLA_HUMAN DNA polymerase alpha catalytic subunit (Gene Name=POLA1)

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