Structure of PDB 4ncn Chain A Binding Site BS01

Receptor Information
>4ncn Chain A (length=344) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NKDNLRSPICCILGHVDTGKTKLLDKIRQTNVQEGEAGGITQQIGATYFP
VEAIKQKTAVVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCNIAI
LVVDIMHGLEPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNGFRE
SFALQNKAVQNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLVPTS
AHTGEGIPDMLKLIVQLCQERMASSLMYLSELQATVLEVKAIEGFGVTID
VILSNGILREGDRIVLCGLEGPIKTNIRALLTPAPMRELRIKGQYIHHKE
VKAAQGVKISAPGLEGAIAGSRLLVVGPDDDEEELEEEVESDLQ
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain4ncn Chain A Residue 1001 [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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PDB4ncn eIF5B employs a novel domain release mechanism to catalyze ribosomal subunit joining.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		V532 D533 T534 G535 K536 T537 K538 Q549 I556 T557 G597 N648 K649 D651 R652 S716 A717 H718
Binding residue
(residue number reindexed from 1)		V16 D17 T18 G19 K20 T21 K22 Q33 I40 T41 G81 N132 K133 D135 R136 S200 A201 H202
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=5.67,Kd=2.12uM
Enzymatic activity
Enzyme Commision number 3.6.5.3: protein-synthesizing GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:4ncn, PDBe:4ncn, PDBj:4ncn
PDBsum4ncn
PubMed24686316
UniProtG0S8G9|IF2P_CHATD Eukaryotic translation initiation factor 5B (Gene Name=CTHT_0029840)

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