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(-) Description

Title :  LACTATE DEHYDROGENASE IN COMPLEX WITH INHIBITOR COMPOUND 13
 
Authors :  C. Eigenbrot, M. Ultsch
Date :  22 Aug 14  (Deposition) - 24 Dec 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.19
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Labadie, P. S. Dragovich, J. Chen, B. P. Fauber, J. Boggs, L. B. Corson, C. Z. Ding, C. Eigenbrot, H. Ge, Q. Ho, K. W. Lai, S. Ma, S. Malek, D. Peterson, H. E. Purkey, K. Robarge, L. Salphati, S. Sideris, M. Ultsch, E. Vanderporten, B. Wei, Q. Xu, I. Yen, Q. Yue, H. Zhang, X. Zhang, A. Zhou
Optimization Of 5-(2, 6-Dichlorophenyl)-3-Hydroxy-2-Mercaptocyclohex-2-Enone As Potent Inhibitors Of Human Lactate Dehydrogenase.
Bioorg. Med. Chem. Lett. V. 25 75 2014
PubMed-ID: 25466195  |  Reference-DOI: 10.1016/J.BMCL.2014.11.008

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE A CHAIN
    Chains: A, B, C, D
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LDHA, PIG19
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LDH-A, CELL PROLIFERATION-INDUCING GENE 19 PROTEIN, LDH MUSCLE SUBUNIT, LDH-M, RENAL CARCINOMA ANTIGEN NY-REN-59

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3SO41Ligand/IonSULFATE ION
4W134Ligand/Ion(5R)-2-[(2-CHLOROPHENYL)SULFANYL]-5-[2,6-DICHLORO-3-(TETRAHYDRO-2H-PYRAN-4-YLAMINO)PHENYL]-3-HYDROXYCYCLOHEX-2-EN-1-ONE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:147 , GLY A:151 , PHE A:152 , LYS A:154BINDING SITE FOR RESIDUE EPE A 401
02AC2SOFTWAREGLY A:26 , GLY A:28 , ALA A:29 , VAL A:30 , ASP A:51 , VAL A:52 , ILE A:53 , THR A:94 , ALA A:95 , GLY A:96 , ALA A:97 , ARG A:98 , ILE A:115 , VAL A:135 , SER A:136 , ASN A:137 , LEU A:164 , HIS A:192 , THR A:247 , ILE A:251BINDING SITE FOR RESIDUE NAI A 402
03AC3SOFTWAREARG A:98 , GLN A:99 , ASN A:137 , LEU A:164 , ASP A:165 , ARG A:168 , HIS A:192 , GLY A:193 , ASP A:194 , ALA A:237 , TYR A:238 , ILE A:241 , THR A:247BINDING SITE FOR RESIDUE W13 A 403
04AC4SOFTWARETRP B:147 , GLY B:151 , PRO B:153 , LYS B:154BINDING SITE FOR RESIDUE EPE B 401
05AC5SOFTWAREGLY B:26 , GLY B:28 , ALA B:29 , VAL B:30 , ASP B:51 , VAL B:52 , ILE B:53 , LYS B:56 , THR B:94 , ALA B:95 , GLY B:96 , ALA B:97 , ARG B:98 , ILE B:115 , ILE B:119 , VAL B:135 , SER B:136 , ASN B:137 , LEU B:164 , HIS B:192 , THR B:247 , ILE B:251 , W13 B:403BINDING SITE FOR RESIDUE NAI B 402
06AC6SOFTWAREARG B:98 , ASN B:137 , LEU B:164 , ASP B:165 , ARG B:168 , HIS B:192 , GLY B:193 , ASP B:194 , VAL B:234 , ALA B:237 , TYR B:238 , ILE B:241 , THR B:247 , NAI B:402BINDING SITE FOR RESIDUE W13 B 403
07AC7SOFTWARETRP C:147 , GLY C:151 , PHE C:152 , PRO C:153 , LYS C:154BINDING SITE FOR RESIDUE EPE C 401
08AC8SOFTWAREGLY C:26 , GLY C:28 , ALA C:29 , VAL C:30 , ASP C:51 , VAL C:52 , ILE C:53 , THR C:94 , ALA C:95 , GLY C:96 , ALA C:97 , ARG C:98 , ILE C:115 , VAL C:135 , SER C:136 , ASN C:137 , LEU C:164 , HIS C:192 , THR C:247 , ILE C:251BINDING SITE FOR RESIDUE NAI C 402
09AC9SOFTWAREARG C:98 , GLY C:102 , ASN C:137 , ASP C:165 , ARG C:168 , HIS C:192 , GLY C:193 , ASP C:194 , ALA C:237 , TYR C:238 , ILE C:241 , THR C:247BINDING SITE FOR RESIDUE W13 C 403
10BC1SOFTWAREGLY D:26 , GLY D:28 , ALA D:29 , VAL D:30 , ASP D:51 , VAL D:52 , ILE D:53 , THR D:94 , ALA D:95 , GLY D:96 , ALA D:97 , ARG D:98 , ILE D:115 , ILE D:119 , VAL D:135 , SER D:136 , ASN D:137 , LEU D:164 , HIS D:192 , THR D:247 , ILE D:251BINDING SITE FOR RESIDUE NAI D 801
11BC2SOFTWAREHIS B:185 , ARG D:170 , HIS D:185BINDING SITE FOR RESIDUE SO4 D 802
12BC3SOFTWAREARG D:98 , GLN D:99 , ASN D:137 , ASP D:165 , ARG D:168 , HIS D:192 , GLY D:193 , ASP D:194 , VAL D:234 , ALA D:237 , TYR D:238 , ILE D:241 , THR D:247BINDING SITE FOR RESIDUE W13 D 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R69)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Glu A:14 -Glu A:15
2Asn A:137 -Pro A:138
3Asn B:137 -Pro B:138
4Asn C:137 -Pro C:138
5Asn D:137 -Pro D:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R69)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R69)

(-) Exons   (0, 0)

(no "Exon" information available for 4R69)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee.......hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.....ee...ee.....ee......ee..eehhhhh...........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r69 A   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326     
                                                                                                                             99|                                                                                                                                                                                                                                 
                                                                                                                             106                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r69 B   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327    
                                                                                                                            98|                                                                                                                                                                                                                                 
                                                                                                                            106                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee.......hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.....ee...ee.....ee......ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r69 C   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
                                                                                                                            98|                                                                                                                                                                                                                                     
                                                                                                                            102                                                                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee.......hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r69 D   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
                                                                                                                             99|                                                                                                                                                                                                                               
                                                                                                                             108
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4R69)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R69)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R69)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  4r69
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  LDHA_HUMAN | P00338
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LDHA_HUMAN | P00338: 1i10 4ajp 4jnk 4l4r 4l4s 4m49 4ojn 4okn 4qo7 4qo8 4qsm 4qt0 4r68 4rls 4zvv 5ixs 5ixy

(-) Related Entries Specified in the PDB File

4r68