Structure of PDB 2gcg Chain D Binding Site BS01

Receptor Information
>2gcg Chain D (length=323) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LMKVFVTRRIPAEGRVALARAADCEVEQWDSDEPIPAKELERGVAGAHGL
LCLLSDHVDKRILDAAGANLKVISTMSVGIDHLALDEIKKRGIRVGYTPD
VLTDTTAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPLWLCGYGLTQST
VGIIGLGRIGQAIARRLKPFGVQRFLYTGRQPRPEEAAEFQAEFVSTPEL
AAQSDFIVVACSLTPATEGLCNKDFFQKMKETAVFINISRGDVVNQDDLY
QALASGKIAAAGLDVTSPEPLPTNHPLLTLKNCVILPHIGSATHRTRNTM
SLLAANNLLAGLRGEPMPSELKL
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain2gcg Chain D Residue 2004 [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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PDB2gcg Structural basis of substrate specificity in human glyoxylate reductase/hydroxypyruvate reductase
Resolution2.2 Å
Binding residue
(original residue number in PDB)		V83 T111 G162 R163 I164 G184 R185 R188 C216 S217 T222 I243 R245 D269 H293 G295
Binding residue
(residue number reindexed from 1)		V78 T106 G157 R158 I159 G179 R180 R183 C211 S212 T217 I238 R240 D264 H288 G290
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) L107 R245 D269 E274 H293
Catalytic site (residue number reindexed from 1) L102 R240 D264 E269 H288
Enzyme Commision number 1.1.1.79: glyoxylate reductase (NADP(+)).
1.1.1.81: hydroxypyruvate reductase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008465 hydroxypyruvate reductase (NADH) activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0016618 hydroxypyruvate reductase [NAD(P)H] activity
GO:0030267 glyoxylate reductase (NADPH) activity
GO:0031406 carboxylic acid binding
GO:0042803 protein homodimerization activity
GO:0050661 NADP binding
GO:0051287 NAD binding
GO:0070402 NADPH binding
GO:0120509 hydroxypyruvate reductase (NADPH) activity
Biological Process
GO:0019752 carboxylic acid metabolic process
GO:0043648 dicarboxylic acid metabolic process
GO:0046487 glyoxylate metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005782 peroxisomal matrix
GO:0005829 cytosol
GO:0070062 extracellular exosome
GO:1902494 catalytic complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2gcg, PDBe:2gcg, PDBj:2gcg
PDBsum2gcg
PubMed16756993
UniProtQ9UBQ7|GRHPR_HUMAN Glyoxylate reductase/hydroxypyruvate reductase (Gene Name=GRHPR)

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