Structure of PDB 4i9h Chain A Binding Site BS01

Receptor Information
>4i9h Chain A (length=325) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AALKDQLIHNLLKEEHVPQNKITVVGVGAVGMACAISILMKDLADELALV
DVMEDKLKGEMMDLQHGSLFLRTPKIVSGKDYSVTANSKLVIITAGARQL
NLVQRNVNIFKFIIPNVVKYSPHCKLLVVSNPVDILTYVAWKISGFPKNR
VIGSGCNLDSARFRYLMGERLGVHALSCHGWILGEHGDSSVPVWSGMNVA
GVSLKTLHPELGTDADKEQWKQVHKQVVDSAYEVIKLKGYTTWAIGLSVA
DLAESIMKNLRRVHPISTMLKGLYGIKEDVFLSVPCVLGQNGISDVVKVT
LTSEEEAHLKKSADTLWGIQKELQF
Ligand information
Ligand ID1E4
InChIInChI=1S/C33H31ClFN3O12S/c1-48-27-10-26(21(34)9-23(27)38-28(41)15-51-29-5-3-17(12-37-29)33(46)47)50-14-25(40)31(43)30(42)24(39)13-49-20-7-18(6-19(35)8-20)22-4-2-16(11-36-22)32(44)45/h2-12,24-25,30-31,39-40,42-43H,13-15H2,1H3,(H,38,41)(H,44,45)(H,46,47)/t24-,25-,30-,31-/m1/s1
InChIKeyHTDBANWISVPXTR-KWINWIPXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6COc1cc(c(cc1NC(=O)CSc2ccc(cn2)C(=O)O)Cl)OC[C@H]([C@H]([C@@H]([C@@H](COc3cc(cc(c3)F)c4ccc(cn4)C(=O)O)O)O)O)O
CACTVS 3.370COc1cc(OC[CH](O)[CH](O)[CH](O)[CH](O)COc2cc(F)cc(c2)c3ccc(cn3)C(O)=O)c(Cl)cc1NC(=O)CSc4ccc(cn4)C(O)=O
CACTVS 3.370COc1cc(OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COc2cc(F)cc(c2)c3ccc(cn3)C(O)=O)c(Cl)cc1NC(=O)CSc4ccc(cn4)C(O)=O
ACDLabs 12.01O=C(O)c1ccc(nc1)c4cc(OCC(O)C(O)C(O)C(O)COc2c(Cl)cc(c(OC)c2)NC(=O)CSc3ncc(cc3)C(=O)O)cc(F)c4
OpenEye OEToolkits 1.7.6COc1cc(c(cc1NC(=O)CSc2ccc(cn2)C(=O)O)Cl)OCC(C(C(C(COc3cc(cc(c3)F)c4ccc(cn4)C(=O)O)O)O)O)O
FormulaC33 H31 Cl F N3 O12 S
Name1-O-[3-(5-carboxypyridin-2-yl)-5-fluorophenyl]-6-O-[4-({[(5-carboxypyridin-2-yl)sulfanyl]acetyl}amino)-2-chloro-5-methoxyphenyl]-D-mannitol
ChEMBLCHEMBL2316886
DrugBank
ZINCZINC000095594374
PDB chain4i9h Chain A Residue 401 [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]
PDB4i9h Fragment growing and linking lead to novel nanomolar lactate dehydrogenase inhibitors.
Resolution2.17 Å
Binding residue
(original residue number in PDB)		G26 G28 V30 D51 V52 T94 A95 G96 R111 N114 I115 F118 V135 S136 N137 R168 A237 T247
Binding residue
(residue number reindexed from 1)		G26 G28 V30 D51 V52 T94 A95 G96 R105 N108 I109 F112 V129 S130 N131 R162 A231 T241
Annotation score1
Binding affinityMOAD: Kd=0.068uM
PDBbind-CN: -logKd/Ki=7.17,Kd=0.068uM
Enzymatic activity
Catalytic site (original residue number in PDB) D165 R168 H192
Catalytic site (residue number reindexed from 1) D159 R162 H186
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:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Biological Process
GO:0006089 lactate metabolic process
GO:0006090 pyruvate metabolic process
GO:0019752 carboxylic acid metabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4i9h, PDBe:4i9h, PDBj:4i9h
PDBsum4i9h
PubMed23302067
UniProtP13491|LDHA_RABIT L-lactate dehydrogenase A chain (Gene Name=LDHA)

[Back to BioLiP]