Structure of PDB 1pkx Chain C Binding Site BS01

Receptor Information

>1pkx Chain C (length=587) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GQLALFSVSDKTGLVEFARNLTALGLNLVASGGTAKALRDAGLAVRDVSE
LTGFPEMLGGRVKTLHPAVHAGILARNIPEDNADMARLDFNLIRVVACNL
YPFVKTVASPGVTVEEAVEQIDIGGVTLLRAAAKNHARVTVVCEPEDYVV
VSTEMQSSESKDTSLETRRQLALKAFTHTAQYDEAISDYFRKQYSKGVSQ
MPLRYGMNPHQTPAQLYTLQPKLPITVLNGAPGFINLCDALNAWQLVKEL
KEALGIPAAASFKHVSPAGAAVGIPLSEDEAKVCMVYDLYKTLTPISAAY
ARARGADRMSSFGDFVALSDVCDVPTAKIISREVSDGIIAPGYEEEALTI
LSKKKNGNYCVLQMDQSYKPDENEVRTLFGLHLSQKRNNGVVDKSLFSNV
VTKNKDLPESALRDLIVATIAVKYTQSNSVCYAKNGQVIGIGAGQQSRIH
CTRLAGDKANYWWLRHHPQVLSMKFKTKRAEISNAIDQYVTGTIGEDEDL
IKWKALFEEVPELLTEAEKKEWVEKLTEVSISSDAFFPFRDNVDRAKRSG
VAYIAAPSGSAADKVVIEACDELGIILAHTNLRLFHH

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

Software	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

ChEMBL

DrugBank

ZINC

PDB chain

1pkx Chain C Residue 1903 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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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)	S7 V8 S9 S31 G33 T34 R61 K63 T64 N99 L100 Y101 D122 I123 G124 G125
Annotation score	2
Binding affinity	MOAD: Ki=0.12uM

Enzymatic activity

Catalytic site (original residue number in PDB)	K266 H267 N431 H592
Catalytic site (residue number reindexed from 1)	K263 H264 N428 H587
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

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Molecular Function

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Cellular Component

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)

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