Structure of PDB 1kep Chain B Binding Site BS02

Receptor Information

>1kep Chain B (length=346) Species: 1307 (Streptococcus suis)

SQFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAI
LGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHT
NFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTA
ETNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKF
IPRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYL
IGADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDE
LGWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVI

Ligand information

• Ligand ID: TDX
• InChI: InChI=1S/C15H24N2O15P2/c1-6-3-17(15(23)16-13(6)22)10-2-7(18)9(30-10)5-29-33(24,25)32-34(26,27)31-14-12(21)11(20)8(19)4-28-14/h3,7-12,14,18-21H,2,4-5H2,1H3,(H,24,25)(H,26,27)(H,16,22,23)/t7-,8+,9+,10+,11-,12+,14+/m0/s1
• InChIKey: AJUADKZRQSBUAK-KDGZBOQCSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O
  CACTVS 3.341: CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3OC[CH](O)[CH](O)[CH]3O)O2)C(=O)NC1=O
  ACDLabs 10.04: O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
  CACTVS 3.341: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(CO3)O)O)O)O
• Formula: C15 H24 N2 O15 P2
• Name: THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE
• DrugBank: DB03161
• ZINC: ZINC000015634247
• PDB chain: 1kep Chain B Residue 4500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1kep Toward a structural understanding of the dehydratase mechanism.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): S86 T125 E127 Y161 N190 K200 F201 R204 Q205 K216 Y218 R225 N260 R284 H287
• Binding residue (residue number reindexed from 1): S85 T124 E126 Y160 N189 K199 F200 R203 Q204 K215 Y217 R224 N259 R283 H286
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): T125 D126 E127 Y161 K165
• Catalytic site (residue number reindexed from 1): T124 D125 E126 Y160 K164
• Enzyme Commision number: 4.2.1.46: dTDP-glucose 4,6-dehydratase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008460 dTDP-glucose 4,6-dehydratase activity
• GO:0016829 lyase activity

Biological Process

• GO:0009225 nucleotide-sugar metabolic process

External links

• PDB: RCSB:1kep, PDBe:1kep, PDBj:1kep
• PDBsum: 1kep
• PubMed: 11796113
• UniProt: Q8GIP9