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Structure of PDB 1wtc Chain A Binding Site BS03

Receptor Information

>1wtc Chain A (length=318) Species: 4896 (Schizosaccharomyces pombe)

VLPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGA
FKFRGALNALSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMP
LDAPEAKVAATKGYGGQVIMYDRYKDDREKMAKEISEREGLTIIPPYDHP
HVLAGQGTAAKELFEEVGPLDALFVCLGGGGLLSGSALAARHFAPNCEVY
GVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVD
DILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGI
IISGGNVDIERYAHFLSQ

Ligand information

• Ligand ID: ACP
• InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
• InChIKey: UFZTZBNSLXELAL-IOSLPCCCSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C11 H18 N5 O12 P3
• Name: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
  ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
• ChEMBL: CHEMBL133463
• DrugBank: DB03909
• ZINC: ZINC000008295124
• PDB chain: 1wtc Chain A Residue 370

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1wtc Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): N25 K52 M53 A114 A115 Y119
• Binding residue (residue number reindexed from 1): N20 K47 M48 A109 A110 Y114
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K57 S82 E208 G212 D214 G236 I307 S308
• Catalytic site (residue number reindexed from 1): K52 S77 E203 G207 D209 G231 I302 S303
• Enzyme Commision number: 4.3.1.17: L-serine ammonia-lyase.
  4.3.1.18: D-serine ammonia-lyase.
  5.1.1.18: serine racemase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0003941 L-serine ammonia-lyase activity
• GO:0005524 ATP binding
• GO:0008721 D-serine ammonia-lyase activity
• GO:0016829 lyase activity
• GO:0016853 isomerase activity
• GO:0018114 threonine racemase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0030378 serine racemase activity
• GO:0042803 protein homodimerization activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006563 L-serine metabolic process
• GO:0070178 D-serine metabolic process

Cellular Component

• GO:0005575 cellular_component

External links

• PDB: RCSB:1wtc, PDBe:1wtc, PDBj:1wtc
• PDBsum: 1wtc
• PubMed: 19640845
• UniProt: O59791|SRR_SCHPO Serine racemase (Gene Name=sry1)

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