Structure of PDB 1r5n Chain A Binding Site BS01

Receptor Information

>1r5n Chain A (length=408) Species: 4896 (Schizosaccharomyces pombe)

TEDATDLQNEVDQELLKDMYGKEHVNIVFIGHVDAGKSTLGGNILFLTGM
VDKRTMEKIEREAKRAYFETEHRRFSLLDAPGASQADIGVLVISARRGEF
EAGFERGGQTREHAVLARTQGINHLVVVINKMDEPSVQWSEERYKECVDK
LSMFLRRVAGYNSKTDVKYMPVSAYTGQNVKDRVDSSVCPWYQGPSLLEY
LDSMTHLERKVNAPFIMPIASKYKDLGTILEGKIEAGSIKKNSNVLVMPI
NQTLEVTAIYDEADEEISSSICGDQVRLRVRGDDSDVQTGYVLTSTKNPV
HATTRFIAQIAILELPSILTTGYSCVMHIHTAVEEVSFAKLLHKLDKTNR
KSKKPPMFATKGMKIIAELETQTPVCMERFEDYQYMGRFTLRDQGTTVAV
GKVVKILD

Ligand information

• Ligand ID: GDP
• InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: QGWNDRXFNXRZMB-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
• Formula: C10 H15 N5 O11 P2
• Name: GUANOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL384759
• DrugBank: DB04315
• ZINC: ZINC000008215481
• PDB chain: 1r5n Chain A Residue 663

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1r5n Crystal structure and functional analysis of the eukaryotic class II release factor eRF3 from S. pombe
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): V247 D248 G250 K251 S252 T253 K278 N384 K385 D387 E388 S427 Y429
• Binding residue (residue number reindexed from 1): V33 D34 G36 K37 S38 T39 K64 N130 K131 D133 E134 S173 Y175
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=5.42,Kd=3.8uM

Enzymatic activity

• Catalytic site (original residue number in PDB): D248 K251 S252
• Catalytic site (residue number reindexed from 1): D34 K37 S38
• Enzyme Commision number: 3.6.5.-

Gene Ontology

Molecular Function

• GO:0003747 translation release factor activity
• GO:0003924 GTPase activity
• GO:0005525 GTP binding

Biological Process

• GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
• GO:0006415 translational termination

External links

• PDB: RCSB:1r5n, PDBe:1r5n, PDBj:1r5n
• PDBsum: 1r5n
• PubMed: 15099522
• UniProt: O74718|ERF3_SCHPO Eukaryotic peptide chain release factor GTP-binding subunit (Gene Name=sup35)