Structure of PDB 1ky4 Chain D Binding Site BS02

Receptor Information
>1ky4 Chain D (length=428) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPYKVADIGLAAWGRKALDIAENEMPGLMRMREMYSASKPLKGARIAGCL
HMTVETAVLIETLVALGAEVRWSSCNIFSTQDHAAAAIAKAGIPVFAWKG
ETDEEYLWCIEQTLHFKDGPLNMILDDGGDLTNLIHTKHPQLLSGIRGIS
EETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIK
RATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAM
EGYEVTTMDEACKEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDV
EIDVKWLNENAVEKVNIKPQVDRYLLKNGHRIILLAEGRLVNLGCAMGHP
SFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNV
KLTKLTEKQAQYLGMPINGPFKPDHYRY
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain1ky4 Chain D Residue 3432 [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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PDB1ky4 Catalytic Mechanism of S-adenosylhomocysteine Hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D3189 N3190 C3194 G3221 V3223 T3241 E3242 I3243 N3247 T3274 T3275 I3280 I3298 G3299 L3343 N3345 H3352
Binding residue
(residue number reindexed from 1)		D186 N187 C191 G218 V220 T238 E239 I240 N244 T271 T272 I277 I295 G296 L340 N342 H349
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H3054 S3077 S3082 D3130 E3155 N3180 K3185 D3189 N3190 C3194 H3300 H3352 S3360 Q3364
Catalytic site (residue number reindexed from 1) H51 S74 S79 D127 E152 N177 K182 D186 N187 C191 H297 H349 S357 Q361
Enzyme Commision number 3.13.2.1: adenosylhomocysteinase.
Gene Ontology
Molecular Function
GO:0004013 adenosylhomocysteinase activity
GO:0005507 copper ion binding
GO:0016787 hydrolase activity
GO:0030554 adenyl nucleotide binding
GO:0042802 identical protein binding
GO:0051287 NAD binding
GO:0098604 adenosylselenohomocysteinase activity
Biological Process
GO:0001666 response to hypoxia
GO:0002439 chronic inflammatory response to antigenic stimulus
GO:0006730 one-carbon metabolic process
GO:0007584 response to nutrient
GO:0019510 S-adenosylhomocysteine catabolic process
GO:0033353 S-adenosylmethionine cycle
GO:0042745 circadian sleep/wake cycle
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0042470 melanosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1ky4, PDBe:1ky4, PDBj:1ky4
PDBsum1ky4
PubMed11927587
UniProtP10760|SAHH_RAT Adenosylhomocysteinase (Gene Name=Ahcy)

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