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(-) Description

Title :  LACTATE DEHYDROGENASE IN COMPLEX WITH HYDROXYLACTAM INHIBITOR COMPOUND 9: (6R)-3-[(2-CHLOROPHENYL)SULFANYL]-4-HYDROXY-6-(3-HYDROXYPHENYL)-6-(THIOPHEN-3-YL)-5,6-DIHYDROPYRIDIN-2(1H)-ONE
 
Authors :  M. Ultsch, C. Eigenbrot
Date :  23 Mar 16  (Deposition) - 14 Sep 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase Tetramer, Oxireductase-Oxireductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. E. Purkey, K. Robarge, J. Chen, Z. Chen, L. B. Corson, C. Z. Ding, A. G. Dipasquale, P. S. Dragovich, C. Eigenbrot, M. Evangelista, B. P. Fauber, Z. Gao, H. Ge, A. Hitz, Q. Ho, S. S. Labadie, K. W. Lai, W. Liu Y. Liu, C. Li, S. Ma, S. Malek, T. O'Brien, J. Pang, D. Peterson, L. Salphati, S. Sideris, M. Ultsch, B. Wei, I. Yen, Q. Yue, H. Zhang, A. Zhou
Cell Active Hydroxylactam Inhibitors Of Human Lactate Dehydrogenase With Oral Bioavailability In Mice.
Acs Med. Chem. Lett. V. 7 896 2016
PubMed-ID: 27774125  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00190

(-) 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
16EY4Ligand/Ion(6R)-3-[(2-CHLOROPHENYL)SULFANYL]-4-HYDROXY-6-(3-HYDROXYPHENYL)-6-(THIOPHEN-3-YL)-5,6-DIHYDROPYRIDIN-2(1H)-ONE
2EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
4SO44Ligand/IonSULFATE ION
5TXD3Ligand/Ion1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:147 , GLY A:151 , PRO A:153 , LYS A:154binding site for residue EPE A 401
02AC2SOFTWAREGLY 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 , ASN A:137 , LEU A:164 , HIS A:192 , THR A:247 , ILE A:251 , 6EY A:403 , HOH A:502 , HOH A:507 , HOH A:513 , HOH A:579 , HOH A:592binding site for residue TXD A 402
03AC3SOFTWAREARG A:98 , ASN 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 , TXD A:402 , HOH A:502 , HOH A:599binding site for residue 6EY A 403
04AC4SOFTWAREARG A:170 , HIS A:185 , HOH A:536 , HOH A:538 , HOH A:622 , HIS C:185 , HOH C:522binding site for residue SO4 A 404
05AC5SOFTWARETRP B:147 , GLY B:151 , PHE B:152 , PRO B:153 , LYS B:154binding site for residue EPE B 401
06AC6SOFTWAREGLY 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 , ALA B:97 , ARG B:98 , ILE B:115 , VAL B:135 , ASN B:137 , HIS B:192 , THR B:247 , ILE B:251 , 6EY B:403 , HOH B:512 , HOH B:516 , HOH B:521 , HOH B:562 , HOH B:589 , GLY D:102binding site for residue TXD B 402
07AC7SOFTWAREARG B:98 , ASN B:137 , ASP B:165 , ARG B:168 , HIS B:192 , GLY B:193 , ALA B:237 , TYR B:238 , ILE B:241 , TYR B:246 , THR B:247 , TXD B:402binding site for residue 6EY B 403
08AC8SOFTWAREARG B:170 , HIS B:185 , HOH B:553 , HOH B:573 , HOH B:585 , HOH B:590 , HIS D:185 , HOH D:947binding site for residue SO4 B 404
09AC9SOFTWARETRP C:147 , GLY C:151 , PRO C:153 , LYS C:154 , HOH C:515binding site for residue EPE C 401
10AD1SOFTWAREGLY 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 , VAL C:135 , SER C:136 , ASN C:137 , HIS C:192 , THR C:247 , ILE C:251 , 6EY C:403 , HOH C:501 , HOH C:507 , HOH C:530 , HOH C:549binding site for residue NAI C 402
11AD2SOFTWAREARG C:98 , ASN C:137 , ASP C:165 , ARG C:168 , HIS C:192 , GLY C:193 , ALA C:237 , TYR C:238 , ILE C:241 , TYR C:246 , THR C:247 , NAI C:402 , HOH C:501binding site for residue 6EY C 403
12AD3SOFTWAREHIS A:185 , HOH A:557 , ARG C:170 , HIS C:185 , HOH C:503 , HOH C:537 , HOH C:553binding site for residue SO4 C 404
13AD4SOFTWAREGLY 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:251 , 6EY D:802 , HOH D:903 , HOH D:907 , HOH D:917 , HOH D:957 , HOH D:1019 , HOH D:1024binding site for residue TXD D 801
14AD5SOFTWAREARG D:98 , GLN D:99 , ASN 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 , TXD D:801 , HOH D:907 , HOH D:931binding site for residue 6EY D 802
15AD6SOFTWAREHIS B:185 , ARG D:170 , HIS D:185 , HOH D:932 , HOH D:964 , HOH D:968 , HOH D:970binding site for residue SO4 D 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IXS)

(-) 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 5IXS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IXS)

(-) Exons   (0, 0)

(no "Exon" information available for 5IXS)

(-) 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:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee.......hhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhhhheeeee.......eeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ixs A   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQSRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       
                                                                                                                             99|                                                                                                                                                                                                                                   
                                                                                                                             104                                                                                                                                                                                                                                   


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.hhhhh...ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ixs 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:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh.eeeeee......hhhhhhhhhhhhhhhhhhhhh...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
                 5ixs C   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 D from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               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.hhhhh...ee.......ee.hhh.ee..eehhhhh...........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ixs D   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       100|      111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
                                                                                                                             100|                                                                                                                                                                                                                                     
                                                                                                                              102
   Legend:   → Mismatch (orange background)
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    → 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 5IXS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IXS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IXS)

(-) 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 4qo8 4qsm 4qt0 4r68 4r69 4rls 4zvv 5ixy

(-) Related Entries Specified in the PDB File

5ixy