Structure of PDB 6qv4 Chain A Binding Site BS04

Receptor Information

>6qv4 Chain A (length=1666) Species: 209285 (Thermochaetoides thermophila)

RMPEGTTKRVFKGYEEIHVPPPKKRSDPTDQNIPVTELPEWARIPFNTTK
TLNKIQSKCFPTAFLDDGNMLVCAPTGSGKTNVAMLTMLREIGKNRNEKG
EIDLDAFKIVYIAPLKALVQEQVGNFGKRLEPYGIKVSELTGDRQLTKQQ
ISETQVIVTTPEKWDVITRKATDISYTNLVRLIIIDEIHLLHDDRGPVLE
SIVSRTIRRTEQTGEPVRIIGLSATLPNYRDVASFLRVDFEKGLFYFDGS
YRPCPLRQEFIGVTDKQLKTMNDITYQKVLEHVGQNRNQMLIFVHSRKET
AKTAKYIRDKALEMDTINQILKHDAGTREVLQEAASSVNNTDLKDLLPYG
FGIHHAGMSRADRTDVEDLFASGHIQVLVCTATLAWGVNLPAHTVIIKGT
QVYSPEKGSWVELSPQDVLQMLGRAGRPQYDTYGEGIIITTQGEIPYYLS
LLNQQLPIESQLVSKLVDSLNAEIVLGNVRNRDEGVEWLGYTYLFVRMLR
SPGLYSVGAEYEDDVALEQKRVDLIHSAAMVLKKSNLIKYDEKTGKMQAT
ELGRIASHYYISHESMDTYNKLIHPAMNDVELFRVFAQSGEFKYIPVRQE
EKLELAKLLARVPIPVKESIEEPTAKINVLLQAYISRLKLEGLALMADMV
YVTQSAGRILRAIFEICLKKGWASVAKLALNMCKMAEKRMWPTMSPLRQY
PTCPAEIIKKAERMDVPWSSYFDLDPPRMGELLGMPKAGKTVCALVSKFP
RVEIQGNVQPMTRSMLRIELTITPNFQWDVELHGVTESFWILVEDCDGEE
ILFHDVFILRKDLAEAEENEHTVEFTVPISEPMPPNYFISVISDRWMHSE
TRMPVSFQKLILPERFPPHTELLDLQPLPVSALKAKDYAALYPNWQQFNK
IQTQTFNSLYNTDNNVLVAAPTGSGKTVCAEFALLRHWAKKDAGRAVYIA
PFQELVDLRFQDWQKRLSHLRGGKEIVKLTGETTTDLKLLEQGDLILATP
LQWDVLSRQWKRRKNVQTVELFIADDLHMLGGQMGYIYEIVVSRMHFIRT
QTELPMRIVGLSVSLANARDIGEWIDAKKHDIYNFSPHVRPVPLELHIQS
YTIPHFPSLMLAMAKPTYLAITQLSPDQPAIVFVPSRKQTRATARDLLTA
CLADDDEDRFLHVEVDQIRKLLDHVQEEALAEALSHGVGYYHEALSQSDK
RIVKHLYNNGAIQVLIASRDVCWELDFTAHLVVVMGTQFFEGKEHRYIDY
PLSEVLQMFGKALQPSKDGRSRGVLMLPAVKREYYKKFLNEALPVESHLH
NFLPDAFVTEISTKMIESGEDAINWATFTYFYRRLLANPSYYGLQDPTHD
GLSQYLSDLVETTLKQLSDARIIEMDEDEGTVAPLNAAMIAAYYNISYMT
MEMFLLSLSHKSKLRTILEIVTAATEFESIQTRRHEEGILKRIYDHVPVK
MNNPVWDSAHFKAFVLVQAHFSRMNLPIDLAKDQEVILQKILSLLSAIVD
ILSSEGHLNALNAMEMSQMVVQAMWDRDSPLKQIPNFTPEVVKVANKYGI
NDIFDFMEQMNPEENPNYASLVKDLGLTQAQLAQAANFTNNKYPDPAYLK
IHIEREFDPTVHAPFYPGKKSENWWLVVGEESTKTLLAIKRVTVELNVKL
EFVFLMSDSYVGVDQD

Ligand information

• Ligand ID: AGS
• InChI: InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
• InChIKey: NLTUCYMLOPLUHL-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C10 H16 N5 O12 P3 S
• Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
  ATP-GAMMA-S;
  ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
  ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
  ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
• ChEMBL: CHEMBL131890
• DrugBank: DB02930
• ZINC: ZINC000008295128
• PDB chain: 6qv4 Chain A Residue 2205

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qv4 Molecular Mechanism Underlying Inhibition of Intrinsic ATPase Activity in a Ski2-like RNA Helicase.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): Y653 I1289 R1291 H1586 F1587 H1726 Y1728 R1915 H1916
• Binding residue (residue number reindexed from 1): Y176 I808 R810 H1105 F1106 H1245 Y1247 R1434 H1435
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity

External links

• PDB: RCSB:6qv4, PDBe:6qv4, PDBj:6qv4
• PDBsum: 6qv4
• PubMed: 31859026
• UniProt: G0S0B9