Structure of PDB 4jnk Chain D Binding Site BS02

Receptor Information
>4jnk Chain D (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 IDZHK
InChIInChI=1S/C20H15Cl2N5O4S2/c1-10(18(28)25-12-3-5-13(6-4-12)33(24,30)31)32-20-26-17(14(9-23)19(29)27-20)11-2-7-15(21)16(22)8-11/h2-8,10H,1H3,(H,25,28)(H2,24,30,31)(H,26,27,29)/t10-/m1/s1
InChIKeyYDJOCTZRWDYNJT-SNVBAGLBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C(=O)Nc1ccc(cc1)S(=O)(=O)N)SC2=NC(=C(C(=O)N2)C#N)c3ccc(c(c3)Cl)Cl
CACTVS 3.385C[C@@H](SC1=NC(=C(C#N)C(=O)N1)c2ccc(Cl)c(Cl)c2)C(=O)Nc3ccc(cc3)[S](N)(=O)=O
ACDLabs 12.01N#CC2=C(N=C(SC(C(=O)Nc1ccc(cc1)S(=O)(=O)N)C)NC2=O)c3ccc(Cl)c(Cl)c3
OpenEye OEToolkits 1.7.6C[C@H](C(=O)Nc1ccc(cc1)S(=O)(=O)N)SC2=NC(=C(C(=O)N2)C#N)c3ccc(c(c3)Cl)Cl
CACTVS 3.385C[CH](SC1=NC(=C(C#N)C(=O)N1)c2ccc(Cl)c(Cl)c2)C(=O)Nc3ccc(cc3)[S](N)(=O)=O
FormulaC20 H15 Cl2 N5 O4 S2
Name(2R)-2-{[5-cyano-4-(3,4-dichlorophenyl)-6-oxo-1,6-dihydropyrimidin-2-yl]sulfanyl}-N-(4-sulfamoylphenyl)propanamide
ChEMBL
DrugBank
ZINCZINC000096269986
PDB chain4jnk Chain D Residue 802 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jnk Identification of substituted 2-thio-6-oxo-1,6-dihydropyrimidines as inhibitors of human lactate dehydrogenase.
Resolution1.896 Å
Binding residue
(original residue number in PDB)		Q99 R105 L108 N137 P138 D140 E191 H192 D194
Binding residue
(residue number reindexed from 1)		Q99 R105 L108 N137 P138 D140 E191 H192 D194
Annotation score1
Binding affinityMOAD: Kd=5.1uM
BindingDB: IC50=750nM,Kd=5100nM
Enzymatic activity
Catalytic site (original residue number in PDB) R105 D165 R168 H192
Catalytic site (residue number reindexed from 1) R105 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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4jnk, PDBe:4jnk, PDBj:4jnk
PDBsum4jnk
PubMed23628333
UniProtP00338|LDHA_HUMAN L-lactate dehydrogenase A chain (Gene Name=LDHA)

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