Structure of PDB 4al4 Chain D Binding Site BS01

Receptor Information
>4al4 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 IDW7E
InChIInChI=1S/C24H26N4O7S/c1-14-27-19-7-4-16(13-20(19)36-14)28-21(29)8-9-25-24(34)26-10-11-35-17-5-2-15(3-6-17)12-18(22(30)31)23(32)33/h2-7,13,18H,8-12H2,1H3,(H,28,29)(H,30,31)(H,32,33)(H2,25,26,34)
InChIKeyYPEMYPUMNYOIMU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1nc2ccc(cc2s1)NC(=O)CCNC(=O)NCCOc3ccc(cc3)CC(C(=O)O)C(=O)O
ACDLabs 12.01O=C(O)C(C(=O)O)Cc3ccc(OCCNC(=O)NCCC(=O)Nc1ccc2nc(sc2c1)C)cc3
CACTVS 3.385Cc1sc2cc(NC(=O)CCNC(=O)NCCOc3ccc(CC(C(O)=O)C(O)=O)cc3)ccc2n1
FormulaC24 H26 N4 O7 S
Name2-[[4-[2-[[3-[(2-methyl-1,3-benzothiazol-6-yl)amino]-3-oxidanylidene-propyl]carbamoylamino]ethoxy]phenyl]methyl]propanedioic acid;
2-[[4-[2-[[3-[(2-methyl-1,3-benzothiazol-6-yl)amino]-3-oxo-propyl]carbamoylamino]ethoxy]phenyl]methyl]propanedioic acid
ChEMBLCHEMBL2059008
DrugBank
ZINCZINC000084687867
PDB chain4al4 Chain D Residue 1332 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4al4 The Design and Synthesis of Novel Lactate Dehydrogenase a Inhibitors by Fragment-Based Lead Generation
Resolution1.78 Å
Binding residue
(original residue number in PDB)		G28 V30 D51 V52 T94 A95 G96 Q99 R105 I115 I119 V135 N137 L164 R168 H192 A237 T247 I251
Binding residue
(residue number reindexed from 1)		G27 V29 D50 V51 T93 A94 G95 Q98 R104 I114 I118 V134 N136 L163 R167 H191 A236 T246 I250
Annotation score1
Binding affinityMOAD: Kd=0.13uM
BindingDB: IC50=4.2e+3nM,Kd=1.3e+2nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4al4, PDBe:4al4, PDBj:4al4
PDBsum4al4
PubMed22417091
UniProtP04642|LDHA_RAT L-lactate dehydrogenase A chain (Gene Name=Ldha)

[Back to BioLiP]