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(-) Description

Title :  LACTATE DEHYDROGENASE A IN COMPLEX WITH SUBSTITUTED 3-HYDROXY-2-MERCAPTOCYCLOHEX-2-ENONE COMPOUND 104
 
Authors :  C. Eigenbrot, M. Ultsch
Date :  19 Jun 14  (Deposition) - 16 Jul 14  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Nicotinamide Adenine Dinucleotide, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Dragovich, B. P. Fauber, J. Boggs, J. Chen, L. B. Corson, C. Z. Ding C. Eigenbrot, H. Ge, A. M. Giannetti, T. Hunsaker, S. Labadie, C. Li, Y. Liu, Y. Liu, S. Ma, S. Malek, D. Peterson, K. E. Pitts, H. E. Purkey, K. Robarge, L. Salphati, S. Sideris, M. Ultsch, E. Vanderporten, J. Wang, B. Wei, Q. Xu, I. Yen, Q. Yue, H. Zhang, X. Zhang, A. Zhou
Identification Of Substituted 3-Hydroxy-2-Mercaptocyclohex-2-Enones As Potent Inhibitors Of Human Lactate Dehydrogenase.
Bioorg. Med. Chem. Lett. V. 24 3764 2014
PubMed-ID: 25037916  |  Reference-DOI: 10.1016/J.BMCL.2014.06.076

(-) 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, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
136U3Ligand/Ion(5S)-2-[(2-CHLOROPHENYL)SULFANYL]-5-(2,6-DICHLOROPHENYL)-3-HYDROXYCYCLOHEX-2-EN-1-ONE
2EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3LAC1Ligand/IonLACTIC ACID
4NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
5SO44Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
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 , ARG A:98 , ILE A:115 , ILE A:119 , VAL A:135 , SER A:136 , ASN A:137 , SER A:160 , HIS A:192 , THR A:247 , ILE A:251 , 36U A:804 , HOH A:906 , HOH A:910 , HOH A:931 , HOH A:950 , HOH A:999 , HOH A:1004 , HOH A:1043 , HOH A:1073BINDING SITE FOR RESIDUE NAI A 801
02AC2SOFTWARETRP A:147 , GLY A:151 , PHE A:152 , LYS A:154 , HOH A:1075BINDING SITE FOR RESIDUE EPE A 802
03AC3SOFTWAREARG A:170 , HIS A:185 , HOH A:935 , HOH A:940 , HOH A:1005 , HOH A:1051 , HIS C:185BINDING SITE FOR RESIDUE SO4 A 803
04AC4SOFTWAREASN A:137 , ASP A:165 , ARG A:168 , HIS A:192 , GLY A:193 , ALA A:237 , TYR A:238 , ILE A:241 , THR A:247 , NAI A:801BINDING SITE FOR RESIDUE 36U 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:901 , HOH B:903 , HOH B:905 , HOH B:925 , HOH B:944 , HOH B:952 , HOH B:1017 , HOH B:1058 , HOH B:1141BINDING SITE FOR RESIDUE NAI B 801
06AC6SOFTWARELYS A:283 , TRP B:147 , GLY B:151 , PRO B:153 , LYS B:154 , HOH B:1115BINDING 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:801BINDING SITE FOR RESIDUE LAC B 803
08AC8SOFTWAREARG B:170 , HIS B:185 , HOH B:940 , HOH B:986 , HOH B:1023 , HIS D:185 , HOH D:902BINDING SITE FOR RESIDUE SO4 B 804
09AC9SOFTWAREGLY 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 , ILE C:115 , VAL C:135 , SER C:136 , ASN C:137 , HIS C:192 , THR C:247 , 36U C:804 , HOH C:928 , HOH C:933 , HOH C:955 , HOH C:969 , HOH C:972BINDING SITE FOR RESIDUE NAI C 801
10BC1SOFTWARETRP C:147 , GLY C:151 , PHE C:152 , PRO C:153 , LYS C:154BINDING SITE FOR RESIDUE EPE C 802
11BC2SOFTWARELEU A:182 , HIS A:185 , HOH A:1068 , ARG C:170 , HIS C:185 , HOH C:932 , HOH C:934 , HOH C:1024 , HOH C:1029 , HOH C:1039BINDING SITE FOR RESIDUE SO4 C 803
12BC3SOFTWAREASN C:137 , ASP C:165 , ARG C:168 , HIS C:192 , GLY C:193 , ALA C:237 , TYR C:238 , NAI C:801 , HOH C:1031BINDING SITE FOR RESIDUE 36U C 804
13BC4SOFTWAREGLU C:101 , GLY D:28 , ALA D:29 , VAL D:30 , ASP D:51 , VAL D:52 , ILE D:53 , THR D:94 , ALA D:95 , ILE D:115 , ILE D:119 , VAL D:135 , ASN D:137 , SER D:160 , HIS D:192 , THR D:247 , 36U D:803 , HOH D:912 , HOH D:930 , HOH D:942 , HOH D:1001 , HOH D:1015 , HOH D:1043 , HOH D:1051BINDING SITE FOR RESIDUE NAI D 801
14BC5SOFTWAREHIS B:185 , ARG D:170 , HIS D:185 , HOH D:901 , HOH D:911 , HOH D:937BINDING SITE FOR RESIDUE SO4 D 802
15BC6SOFTWAREASN D:137 , ASP D:165 , ARG D:168 , HIS D:192 , GLY D:193 , ALA D:237 , TYR D:238 , ILE D:241 , THR D:247 , NAI D:801 , HOH D:1015BINDING SITE FOR RESIDUE 36U D 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QO8)

(-) 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 4QO8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QO8)

(-) Exons   (0, 0)

(no "Exon" information available for 4QO8)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                           
               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.hhh.ee..ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qo8 A   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 B from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               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.hhh.ee..ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qo8 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.eeeeee.......eeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qo8 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4qo8 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)
  - → 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 4QO8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QO8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QO8)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4qsm 4qt0 4r68 4r69 4rls 4zvv 5ixs 5ixy

(-) Related Entries Specified in the PDB File

4qo7