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Structure of PDB 3nl6 Chain A Binding Site BS02

Receptor Information

>3nl6 Chain A (length=518) Species: 5478 (Nakaseomyces glabratus)

KFSKEQFDYSLYLVTSGMIPEGKTLYGQVEAGLQNGVTLVQIREKDADTK
FFIEEALQIKELCHAHNVPLIINDRIDVAMAIGADGIHVGQDDMPIPMIR
KLVGPDMVIGWSVGFPEEVDELSKMGPVDYIGVGTLFPTLTKKAPMGTAG
AIRVLDALERNNAHWCRTVGIGGLHPDNIERVLYQCVSSNGKRSLDGICV
VSDIIASLDAAKSTKILRGLIDKTDYKFVNIGLSTKNSLTTTDEIQSIIS
NTLKARPLVQHITNKVHQNFGANVTLALGSSPIMSEIQSEVNDLAAIPHA
TLLLNTGSVAPPEMLKAAIRAYNDVKRPIVFDPVGYSATETRLLLNNKLL
TFGQFSCIKGNSSEILGLAELSNELLIQATKIVAFKYKTVAVCTGEFDFI
ADGTIEGKYSLSKGTNGTSVEDIPCVAVEAGPIEIMGDITASGCSLGSTI
ACMIGGQPSEGNLFHAVVAGVMLYKAAGKIASEKCNGSGSFQVELIDALY
RLTRENTPVTWAPKLTHT

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: 3nl6 Chain A Residue 799

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nl6 Domain Organization in Candida glabrata THI6, a Bifunctional Enzyme Required for Thiamin Biosynthesis in Eukaryotes .
• Resolution: 2.612 Å
• Binding residue (original residue number in PDB): N369 T416 G417 E418 D420 I455 M458 A463 S464 G465 Y496 K497
• Binding residue (residue number reindexed from 1): N361 T394 G395 E396 D398 I433 M436 A441 S442 G443 Y474 K475
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): R45 S114
• Catalytic site (residue number reindexed from 1): R43 S112
• Enzyme Commision number: 2.5.1.3: thiamine phosphate synthase.
  2.7.1.50: hydroxyethylthiazole kinase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004417 hydroxyethylthiazole kinase activity
• GO:0004789 thiamine-phosphate diphosphorylase activity
• GO:0005524 ATP binding
• GO:0016740 transferase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0009228 thiamine biosynthetic process
• GO:0009229 thiamine diphosphate biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:3nl6, PDBe:3nl6, PDBj:3nl6
• PDBsum: 3nl6
• PubMed: 20968298
• UniProt: Q6FV03

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