Structure of PDB 5n6c Chain B Binding Site BS01

Receptor Information
>5n6c Chain B (length=299) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSAT
KVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAA
ELTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLGILGLGRIG
REVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFITVHT
PLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGA
ALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIAVQFVDM
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 chain5n6c Chain B Residue 401 [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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PDB5n6c Structural insights into the enzymatic activity and potential substrate promiscuity of human 3-phosphoglycerate dehydrogenase (PHGDH).
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G152 G154 R155 I156 Y174 D175 P176 I177 H206 T207 P208 T213 C234 A235 R236 H283 G285
Binding residue
(residue number reindexed from 1)		G145 G147 R148 I149 Y167 D168 P169 I170 H199 T200 P201 T206 C227 A228 R229 H276 G278
Annotation score4
Binding affinityMOAD: Ka=22500M^-1
Enzymatic activity
Catalytic site (original residue number in PDB) N102 R236 D260 E265 H283
Catalytic site (residue number reindexed from 1) N95 R229 D253 E258 H276
Enzyme Commision number 1.1.1.37: malate dehydrogenase.
1.1.1.399: 2-oxoglutarate reductase.
1.1.1.95: phosphoglycerate dehydrogenase.
Gene Ontology
Molecular Function
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding

View graph for
Molecular Function
External links
PDB RCSB:5n6c, PDBe:5n6c, PDBj:5n6c
PDBsum5n6c
PubMed29262655
UniProtO43175|SERA_HUMAN D-3-phosphoglycerate dehydrogenase (Gene Name=PHGDH)

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