Structure of PDB 1pkx Chain A Binding Site BS01

Receptor Information

>1pkx Chain A (length=588) Species: 9606 (Homo sapiens)

PGQLALFSVSDKTGLVEFARNLTALGLNLVASGGTAKALRDAGLAVRDVS
ELTGFPEMLGGRVKTLHPAVHAGILARNIPEDNADMARLDFNLIRVVACN
LYPFVKTVASPGVTVEEAVEQIDIGGVTLLRAAAKNHARVTVVCEPEDYV
VVSTEMQSSESKDTSLETRRQLALKAFTHTAQYDEAISDYFRKQYSKGVS
QMPLRYGMNPHQTPAQLYTLQPKLPITVLNGAPGFINLCDALNAWQLVKE
LKEALGIPAAASFKHVSPAGAAVGIPLSEDEAKVCMVYDLYKTLTPISAA
YARARGADRMSSFGDFVALSDVCDVPTAKIISREVSDGIIAPGYEEEALT
ILSKKKNGNYCVLQMDQSYKPDENEVRTLFGLHLSQKRNNGVVDKSLFSN
VVTKNKDLPESALRDLIVATIAVKYTQSNSVCYAKNGQVIGIGAGQQSRI
HCTRLAGDKANYWWLRHHPQVLSMKFKTGVAEISNAIDQYVTGTIGEDED
LIKWKALFEEVPELLTEAEKKEWVEKLTEVSISSDAFFPFRDNVDRAKRS
GVAYIAAPSGSAADKVVIEACDELGIILAHTNLRLFHH

Ligand information

• Ligand ID: XMP
• InChI: InChI=1S/C10H13N4O9P/c15-5-3(1-22-24(19,20)21)23-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H2,19,20,21)(H2,12,13,17,18)/p+1/t3-,5-,6-,9-/m1/s1
• InChIKey: DCTLYFZHFGENCW-UUOKFMHZSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: c1[nH+]c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)NC(=O)NC2=O
  CACTVS 3.341: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2c[nH+]c3C(=O)NC(=O)Nc23
  OpenEye OEToolkits 1.5.0: c1[nH+]c2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)NC(=O)NC2=O
  ACDLabs 10.04: O=C3Nc1c([nH+]cn1C2OC(C(O)C2O)COP(=O)(O)O)C(=O)N3
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2c[nH+]c3C(=O)NC(=O)Nc23
• Formula: C10 H14 N4 O9 P
• Name: XANTHOSINE-5'-MONOPHOSPHATE;
  5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE
• PDB chain: 1pkx Chain A Residue 1901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1pkx Structural Insights into the Human and Avian IMP Cyclohydrolase Mechanism via Crystal Structures with the Bound XMP Inhibitor.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): S10 V11 S12 S34 G36 T37 R64 K66 T67 N102 L103 Y104 D125 I126 G127 G128
• Binding residue (residue number reindexed from 1): S8 V9 S10 S32 G34 T35 R62 K64 T65 N100 L101 Y102 D123 I124 G125 G126
• Annotation score: 2
• Binding affinity: MOAD: Ki=0.12uM
  PDBbind-CN: -logKd/Ki=6.92,Ki=0.12uM

Enzymatic activity

• Catalytic site (original residue number in PDB): K266 H267 N431 H592
• Catalytic site (residue number reindexed from 1): K264 H265 N429 H588
• Enzyme Commision number: 2.1.2.3: phosphoribosylaminoimidazolecarboxamide formyltransferase.
  3.5.4.10: IMP cyclohydrolase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0003937 IMP cyclohydrolase activity
• GO:0004643 phosphoribosylaminoimidazolecarboxamide formyltransferase activity
• GO:0016740 transferase activity
• GO:0016787 hydrolase activity
• GO:0042803 protein homodimerization activity
• GO:0045296 cadherin binding

Biological Process

• GO:0003360 brainstem development
• GO:0006139 nucleobase-containing compound metabolic process
• GO:0006164 purine nucleotide biosynthetic process
• GO:0006177 GMP biosynthetic process
• GO:0006189 'de novo' IMP biosynthetic process
• GO:0021549 cerebellum development
• GO:0021987 cerebral cortex development
• GO:0031100 animal organ regeneration
• GO:0044208 'de novo' AMP biosynthetic process
• GO:0046452 dihydrofolate metabolic process
• GO:0046654 tetrahydrofolate biosynthetic process
• GO:0097294 'de novo' XMP biosynthetic process
• GO:0098761 cellular response to interleukin-7

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:1pkx, PDBe:1pkx, PDBj:1pkx
• PDBsum: 1pkx
• PubMed: 14756553
• UniProt: P31939|PUR9_HUMAN Bifunctional purine biosynthesis protein ATIC (Gene Name=ATIC)