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(-) Description

Title :  LACTATE DEHYDROGENASE A IN COMPLEX WITH INHIBITOR COMPOUND 22
 
Authors :  C. Eigenbrot, M. Ultsch
Date :  15 Mar 13  (Deposition) - 22 May 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha-Beta, Pyruvate Reductase And Lactate Dehydrogenase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Dragovich, B. P. Fauber, L. B. Corson, C. Z. Ding, C. Eigenbrot, H. Ge, A. M. Giannetti, T. Hunsaker, S. Labadie, Y. Liu, S. Malek, B. Pan D. Peterson, K. Pitts, H. E. Purkey, S. Sideris, M. Ultsch, E. Vanderporten, B. Wei, Q. Xu, I. Yen, Q. Yue, H. Zhang, X. Zhang
Identification Of Substituted 2-Thio-6-Oxo-1, 6-Dihydropyrimidines As Inhibitors Of Human Lactate Dehydrogenase.
Bioorg. Med. Chem. Lett. V. 23 3186 2013
PubMed-ID: 23628333  |  Reference-DOI: 10.1016/J.BMCL.2013.04.001

(-) 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  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2LAC1Ligand/IonLACTIC ACID
3NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
4SO43Ligand/IonSULFATE ION
5ZHK3Ligand/Ion(2R)-2-{[5-CYANO-4-(3,4-DICHLOROPHENYL)-6-OXO-1,6-DIHYDROPYRIMIDIN-2-YL]SULFANYL}-N-(4-SULFAMOYLPHENYL)PROPANAMIDE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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:119 , VAL A:135 , SER A:136 , ASN A:137 , SER A:160 , LEU A:164 , HIS A:192 , THR A:247 , ILE A:251 , ZHK A:803 , HOH A:904 , HOH A:910 , HOH A:926 , HOH A:943 , HOH A:974 , HOH A:986 , HOH A:1058 , HOH A:1067 , HOH A:1082BINDING SITE FOR RESIDUE NAI A 801
02AC2SOFTWARETRP A:147 , GLY A:151 , PHE A:152 , PRO A:153 , LYS A:154 , HOH A:1111BINDING SITE FOR RESIDUE EPE A 802
03AC3SOFTWAREALA A:97 , ARG A:98 , ARG A:105 , LEU A:108 , ASN A:137 , PRO A:138 , VAL A:139 , ASP A:140 , ILE A:141 , GLU A:191 , HIS A:192 , ASP A:194 , TYR A:238 , LEU A:322 , NAI A:801BINDING SITE FOR RESIDUE ZHK A 803
04AC4SOFTWAREARG A:170 , HIS A:185 , HOH A:920 , HOH A:944 , HOH A:978 , HOH A:1146 , HIS C:185 , HOH C:1164BINDING SITE FOR RESIDUE SO4 A 804
05AC5SOFTWAREGLY 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 , GLN B:99 , ILE B:115 , ILE B:119 , VAL B:135 , ASN B:137 , SER B:160 , LEU B:164 , HIS B:192 , THR B:247 , ILE B:251 , LAC B:803 , HOH B:903 , HOH B:904 , HOH B:905 , HOH B:908 , HOH B:915 , HOH B:941 , HOH B:962 , HOH B:1057 , HOH B:1228 , HOH B:1245BINDING SITE FOR RESIDUE NAI B 801
06AC6SOFTWARELYS A:283 , TRP B:147 , GLY B:151 , PHE B:152 , PRO B:153 , LYS B:154BINDING SITE FOR RESIDUE EPE B 802
07AC7SOFTWAREGLN B:99 , ARG B:105 , ASN B:137 , ARG B:168 , HIS B:192 , ALA B:237 , THR B:247 , NAI B:801 , HOH B:1228BINDING SITE FOR RESIDUE LAC B 803
08AC8SOFTWAREGLY 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 , ARG C:98 , ILE C:115 , ILE C:119 , VAL C:135 , ASN C:137 , HIS C:192 , THR C:247 , ILE C:251 , ZHK C:803 , HOH C:912 , HOH C:933 , HOH C:935 , HOH C:945 , HOH C:967 , HOH C:1035 , HOH C:1045 , HOH C:1058 , HOH C:1060 , HOH C:1077 , HOH C:1100 , HOH C:1160BINDING SITE FOR RESIDUE NAI C 801
09AC9SOFTWARETRP C:147 , GLY C:151 , PHE C:152 , PRO C:153 , LYS C:154 , HOH C:1189BINDING SITE FOR RESIDUE EPE C 802
10BC1SOFTWAREARG C:105 , LEU C:108 , VAL C:109 , ASN C:137 , PRO C:138 , VAL C:139 , ASP C:140 , ILE C:141 , GLU C:191 , HIS C:192 , ASP C:194 , TYR C:238 , LEU C:322 , NAI C:801 , HOH C:933 , HOH C:1010 , HOH C:1159 , HOH C:1161BINDING SITE FOR RESIDUE ZHK C 803
11BC2SOFTWARELEU A:182 , HIS A:185 , ARG C:170 , HIS C:185 , HOH C:932 , HOH C:960 , HOH C:973 , HOH C:1056 , HOH C:1164 , HOH C:1196BINDING SITE FOR RESIDUE SO4 C 804
12BC3SOFTWAREGLU C:101 , HOH C:1106 , GLY D:28 , ALA D:29 , VAL D:30 , ASP D:51 , VAL D:52 , ILE D:53 , THR D:94 , ALA D:95 , ARG D:98 , ILE D:115 , ILE D:119 , VAL D:135 , ASN D:137 , SER D:160 , HIS D:192 , THR D:247 , ILE D:251 , ZHK D:802 , HOH D:905 , HOH D:926 , HOH D:938 , HOH D:976 , HOH D:993 , HOH D:1010 , HOH D:1026 , HOH D:1097BINDING SITE FOR RESIDUE NAI D 801
13BC4SOFTWAREGLN D:99 , ARG D:105 , LEU D:108 , ASN D:137 , PRO D:138 , VAL D:139 , ASP D:140 , ILE D:141 , GLU D:191 , HIS D:192 , ASP D:194 , LEU D:322 , NAI D:801 , HOH D:1075 , HOH D:1097BINDING SITE FOR RESIDUE ZHK D 802
14BC5SOFTWAREHIS B:185 , ARG D:170 , HIS D:185 , HOH D:901 , HOH D:906 , HOH D:952 , HOH D:1086 , HOH D:1113 , HOH D:1161BINDING SITE FOR RESIDUE SO4 D 803

(-) SS Bonds  (0, 0)

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

(-) 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 4JNK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JNK)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4jnka1 A:1-159 Lactate dehydrogenase                                                                                                                     d4jnka2 A:160-331 Lactate dehydrogenase                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh....eee..hhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee..hhhhhee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jnk A   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARSRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325      
                                                                                                                            98|                                                                                                                                                                                                                                   
                                                                                                                            104                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4jnkb1 B:1-159 Lactate dehydrogenase                                                                                                                          d4jnkb2 B:160-331 Lactate dehydrogenase                                                                                                                                      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.hhh.ee..ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jnk B   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 


Chain C from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4jnkc1 C:1-159 Lactate dehydrogenase                                                                                                                          d4jnkc2 C:160-331 Lactate dehydrogenase                                                                                                                                      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.hhh.ee..ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jnk C   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 


Chain D from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4jnkd1 D:1-159 Lactate dehydrogenase                                                                                                                          d4jnkd2 D:160-331 Lactate dehydrogenase                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh....eee..hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jnk D   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
   Legend:   → Mismatch (orange background)
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  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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  4jnk
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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 4l4r 4l4s 4m49 4ojn 4okn 4qo7 4qo8 4qsm 4qt0 4r68 4r69 4rls 4zvv 5ixs 5ixy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JNK)