Structure of PDB 4aji Chain D Binding Site BS01

Receptor Information
>4aji Chain D (length=330) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALKDQLIVNLLKEEQVPQNKITVVGVGAVGMACAISILMKDLADELALVD
VIEDKLKGEMMDLQHGSLFLKTPKIVSSKDYSVTANSKLVIITAGARQQE
GESRLNLVQRNVNIFKFIIPNVVKYSPQCKLLIVSNPVDILTYVAWKISG
FPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWS
GVNVAGVSLKSLNPQLGTDADKEQWKDVHKQVVDSAYEVIKLKGYTSWAI
GLSVADLAESIMKNLRRVHPISTMIKGLYGIKEDVFLSVPCILGQNGISD
VVKVTLTPDEEARLKKSADTLWGIQKELQF
Ligand information
Ligand ID88R
InChIInChI=1S/C12H14O6/c1-17-9-4-3-7(6-10(9)18-2)5-8(11(13)14)12(15)16/h3-4,6,8H,5H2,1-2H3,(H,13,14)(H,15,16)
InChIKeyNQKOQSKMBSAXTD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)C(C(=O)O)Cc1cc(OC)c(OC)cc1
OpenEye OEToolkits 1.9.2COc1ccc(cc1OC)CC(C(=O)O)C(=O)O
CACTVS 3.385COc1ccc(CC(C(O)=O)C(O)=O)cc1OC
FormulaC12 H14 O6
Name2-((3,4-DIMETHOXYPHENYL)METHYL))PROPANEDIOIC ACID
ChEMBLCHEMBL2059003
DrugBank
ZINCZINC000004025332
PDB chain4aji Chain D Residue 1332 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4aji The Design and Synthesis of Novel Lactate Dehydrogenase a Inhibitors by Fragment-Based Lead Generation
Resolution1.93 Å
Binding residue
(original residue number in PDB)		V30 R105 N137 R168 H192 A237 T247 I251
Binding residue
(residue number reindexed from 1)		V29 R104 N136 R167 H191 A236 T246 I250
Annotation score1
Binding affinityMOAD: Kd=280uM
BindingDB: Kd=1.000e+6nM,IC50=>5.00e+5nM
Enzymatic activity
Catalytic site (original residue number in PDB) R105 D165 R168 H192
Catalytic site (residue number reindexed from 1) R104 D164 R167 H191
Enzyme Commision number 1.1.1.27: L-lactate dehydrogenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004457 lactate dehydrogenase activity
GO:0004459 L-lactate dehydrogenase activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0019900 kinase binding
GO:0042802 identical protein binding
GO:0051287 NAD binding
Biological Process
GO:0001666 response to hypoxia
GO:0001889 liver development
GO:0006089 lactate metabolic process
GO:0006090 pyruvate metabolic process
GO:0007519 skeletal muscle tissue development
GO:0007584 response to nutrient
GO:0009410 response to xenobiotic stimulus
GO:0009749 response to glucose
GO:0014070 response to organic cyclic compound
GO:0019661 glucose catabolic process to lactate via pyruvate
GO:0019674 NAD metabolic process
GO:0019752 carboxylic acid metabolic process
GO:0042542 response to hydrogen peroxide
GO:0042867 pyruvate catabolic process
GO:0043065 positive regulation of apoptotic process
GO:0043627 response to estrogen
GO:0051591 response to cAMP
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0035686 sperm fibrous sheath
GO:1990204 oxidoreductase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4aji, PDBe:4aji, PDBj:4aji
PDBsum4aji
PubMed22417091
UniProtP04642|LDHA_RAT L-lactate dehydrogenase A chain (Gene Name=Ldha)

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