Structure of PDB 6qv4 Chain A Binding Site BS05

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 2206

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): W1376 Q1383 G1404 S1405 G1406 K1407 T1408 D1506 D1507
• Binding residue (residue number reindexed from 1): W895 Q902 G923 S924 G925 K926 T927 D1025 D1026
• 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