Structure of PDB 1t2a Chain C Binding Site BS03

Receptor Information
>1t2a Chain C (length=338) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYNMK
LHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVG
TLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGA
AKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIY
LGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSV
REFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDF
LQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTN
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain1t2a Chain C Residue 1202 [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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PDB1t2a Crystal Structure and Biophysical Characterization of Human GDP-D-mannose 4,6-dehydratase
Resolution1.84 Å
Binding residue
(original residue number in PDB)		N208 V219 K222 G241 N242 R247 R325 E328
Binding residue
(residue number reindexed from 1)		N177 V188 K191 G210 N211 R216 R294 E297
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T155 S156 E157 Y179 K183
Catalytic site (residue number reindexed from 1) T124 S125 E126 Y148 K152
Enzyme Commision number 4.2.1.47: GDP-mannose 4,6-dehydratase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008446 GDP-mannose 4,6-dehydratase activity
GO:0016829 lyase activity
GO:0042802 identical protein binding
GO:0070401 NADP+ binding
Biological Process
GO:0007219 Notch signaling pathway
GO:0019673 GDP-mannose metabolic process
GO:0042350 GDP-L-fucose biosynthetic process
GO:0042351 'de novo' GDP-L-fucose biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1t2a, PDBe:1t2a, PDBj:1t2a
PDBsum1t2a
PubMed
UniProtO60547|GMDS_HUMAN GDP-mannose 4,6 dehydratase (Gene Name=GMDS)

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