Structure of PDB 5f2r Chain A Binding Site BS01

Receptor Information
>5f2r Chain A (length=381) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLI
GDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKP
YIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYF
NDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVFDLG
GGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGK
DVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDFSETLTRAK
FEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVK
EFFNGKEPSRGINPDEAVAYGAAVQAGVLSG
Ligand information
Ligand IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain5f2r Chain A Residue 501 [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]
PDB5f2r Probing the ATP Site of GRP78 with Nucleotide Triphosphate Analogs.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		G36 T37 T38 Y39 G226 G227 T229 G255 E293 K296 R297 S300 G363 G364 R367
Binding residue
(residue number reindexed from 1)		G10 T11 T12 Y13 G200 G201 T203 G229 E267 K270 R271 S274 G337 G338 R341
Annotation score3
Binding affinityMOAD: Kd=0.000052M
PDBbind-CN: -logKd/Ki=4.28,Kd=52uM
Enzymatic activity
Catalytic site (original residue number in PDB) D34 K96 E201 D224
Catalytic site (residue number reindexed from 1) D8 K70 E175 D198
Enzyme Commision number 3.6.4.10: non-chaperonin molecular chaperone ATPase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0140662 ATP-dependent protein folding chaperone

View graph for
Molecular Function
External links
PDB RCSB:5f2r, PDBe:5f2r, PDBj:5f2r
PDBsum5f2r
PubMed27144892
UniProtP11021|BIP_HUMAN Endoplasmic reticulum chaperone BiP (Gene Name=HSPA5)

[Back to BioLiP]