Structure of PDB 6egs Chain A Binding Site BS02

Receptor Information
>6egs Chain A (length=478) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEAKVRWPDFNQEAYVGGQVESDKLRMDRAIPDTRHDQCQRKQWRVDLPA
TSVVITFHNEARSALLRTVVSVLKKSPPHLIKEIILVDDYSNDPEDGALL
GKIEKVRVLRNDRREGLMRSRVRGADAAQAKVLTFLDSHCECNEHWLEPL
LERVAEDRTRVVSPIIDVINMDNFQYVGASADLKGGFDWNLVFKWDYMTP
EQRRSRQGNPVAPIKTPMIAGGLFVMDKFYFEELGKYDMMMDVWGGENLE
ISFRVWQCGGSLEIIPCSRVGHVFRKQHPYTFPVFARNTRRAAEVWMDEY
KNFYYAAVPSARNVPYGNIQSRLELRKKLSCKPFKWYLENVYPELRVPDH
QDIAFGALQQGTNCLDTLGHFADGVVGVYECHNAGGNQEWALTKEKSVKH
MDLCLTVVDRAPGSLIKLQGCRENDSRQKWEQIEGNSKLRHVGSNLCLDS
RTAKSGGLSVEVCGPALSQQWKFTLNLQ
Ligand information
Ligand IDUD2
InChIInChI=1S/C17H27N3O17P2/c1-6(22)18-10-13(26)11(24)7(4-21)35-16(10)36-39(31,32)37-38(29,30)33-5-8-12(25)14(27)15(34-8)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11+,12-,13-,14-,15-,16-/m1/s1
InChIKeyLFTYTUAZOPRMMI-NESSUJCYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)NC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
CACTVS 3.341CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
CACTVS 3.341CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1O[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.5.0CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
FormulaC17 H27 N3 O17 P2
NameURIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE;
(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
ChEMBL
DrugBankDB02196
ZINCZINC000008551132
PDB chain6egs Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6egs Structural Analysis of a GalNAc-T2 Mutant Reveals an Induced-Fit Catalytic Mechanism for GalNAc-Ts.
Resolution2.7 Å
Binding residue
(original residue number in PDB)
T143 D176 R201 L204 D224 H226 G308 G309 V330 G332 E334 N335 H359 H365
Binding residue
(residue number reindexed from 1)
T56 D89 R114 L117 D137 H139 G221 G222 V243 G245 E247 N248 H272 H278
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=3.59,Kd=260uM
Enzymatic activity
Enzyme Commision number 2.4.1.41: polypeptide N-acetylgalactosaminyltransferase.
External links
PDB RCSB:6egs, PDBe:6egs, PDBj:6egs
PDBsum6egs
PubMed29601100
UniProtQ10471|GALT2_HUMAN Polypeptide N-acetylgalactosaminyltransferase 2 (Gene Name=GALNT2)

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