Structure of PDB 6hq4 Chain B Binding Site BS01

Receptor Information

>6hq4 Chain B (length=368) Species: 264462 (Bdellovibrio bacteriovorus HD100)

QSVDIHKDQIIFSEGDAGDCAYIIEKGRVLIYLTKDKEEIPLTILGEGEI
FGEMALIDNQNRSASVRALEDVRLAIVTKQQVLERVSTADKVVQLLMRVL
LKRLRSALDQIKLENQIFQAFQNKEFELFYQPIVNLKNKTITGCEALLRW
NSPQHGLVSPNLFIDIIENSSMVIPIGHWIINQALKDLRTIQDQLRLNKK
ERMADDFMMSINISGRQFTHSDFVNNLEDLREKHDLHTQNIKLEMTERIM
MDGAIAIDALNQCRSLGYAISIDDFGTGFSGLQYLTQMPISFLKIDRSFV
MKILSDPKSKAVVSSIIHLAHAMDIEVIAEGIEHHEEALVLETLGARFGQ
GYLFSKPVDLGRFLKLIK

Ligand information

• Ligand ID: CMP
• InChI: InChI=1S/C10H12N5O6P/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7-4(20-10)1-19-22(17,18)21-7/h2-4,6-7,10,16H,1H2,(H,17,18)(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
• InChIKey: IVOMOUWHDPKRLL-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(O4)O)O)N
  ACDLabs 10.04: O=P3(OCC4OC(n1c2ncnc(N)c2nc1)C(O)C4O3)O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@](=O)(O4)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]4[CH]3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P@](O)(=O)O[C@H]4[C@H]3O
• Formula: C10 H12 N5 O6 P
• Name: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE;
  CYCLIC AMP;
  CAMP
• ChEMBL: CHEMBL316966
• DrugBank: DB02527
• ZINC: ZINC000003873977
• PDB chain: 6hq4 Chain B Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6hq4 Nucleotide signaling pathway convergence in a cAMP-sensing bacterial c-di-GMP phosphodiesterase.
• Resolution: 2.63 Å
• Binding residue (original residue number in PDB): F17 F56 G57 E58 M59 A60 R67 S68 A69
• Binding residue (residue number reindexed from 1): F12 F51 G52 E53 M54 A55 R62 S63 A64
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=4.65,Kd=22.4uM

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0046872 metal ion binding

External links

• PDB: RCSB:6hq4, PDBe:6hq4, PDBj:6hq4
• PDBsum: 6hq4
• PubMed: 31355487
• UniProt: Q6MLN6