Structure of PDB 5ixy Chain A Binding Site BS02

Receptor Information
>5ixy Chain A (length=331) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALV
DVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQ
EGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKIS
GFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVW
SGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWA
IGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGIS
DLVKVTLTSEEEARLKKSADTLWGIQKELQF
Ligand information
Ligand IDGN2
InChIInChI=1S/C25H23ClN2O3S2/c26-20-3-1-2-4-22(20)33-23-21(29)15-25(27-24(23)30,18-9-14-32-16-18)17-5-7-19(8-6-17)28-10-12-31-13-11-28/h1-9,14,16,29H,10-13,15H2,(H,27,30)/t25-/m0/s1
InChIKeySUFXXEIVBZJOAP-VWLOTQADSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC1=C(Sc2ccccc2Cl)C(=O)N[C](C1)(c3cscc3)c4ccc(cc4)N5CCOCC5
OpenEye OEToolkits 2.0.5c1ccc(c(c1)SC2=C(CC(NC2=O)(c3ccc(cc3)N4CCOCC4)c5ccsc5)O)Cl
OpenEye OEToolkits 2.0.5c1ccc(c(c1)SC2=C(C[C@](NC2=O)(c3ccc(cc3)N4CCOCC4)c5ccsc5)O)Cl
CACTVS 3.385OC1=C(Sc2ccccc2Cl)C(=O)N[C@](C1)(c3cscc3)c4ccc(cc4)N5CCOCC5
FormulaC25 H23 Cl N2 O3 S2
Name(2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one
ChEMBLCHEMBL4589484
DrugBank
ZINCZINC000584905560
PDB chain5ixy Chain A Residue 404 [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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PDB5ixy Cell Active Hydroxylactam Inhibitors of Human Lactate Dehydrogenase with Oral Bioavailability in Mice.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		R98 N137 D165 R168 H192 G193 A237 Y238 I241 T247
Binding residue
(residue number reindexed from 1)		R98 N137 D165 R168 H192 G193 A237 Y238 I241 T247
Annotation score1
Binding affinityBindingDB: IC50=55nM
Enzymatic activity
Catalytic site (original residue number in PDB) D165 R168 H192
Catalytic site (residue number reindexed from 1) D165 R168 H192
Enzyme Commision number 1.1.1.27: L-lactate dehydrogenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic 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:0042802 identical protein binding
GO:0045296 cadherin binding
Biological Process
GO:0006089 lactate metabolic process
GO:0006090 pyruvate metabolic process
GO:0006096 glycolytic process
GO:0019752 carboxylic acid metabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0016020 membrane
GO:0070062 extracellular exosome
GO:1990204 oxidoreductase complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ixy, PDBe:5ixy, PDBj:5ixy
PDBsum5ixy
PubMed27774125
UniProtP00338|LDHA_HUMAN L-lactate dehydrogenase A chain (Gene Name=LDHA)

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