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(-) Description

Title :  LACTATE DEHYDROGENASE IN COMPLEX WITH HYDROXYLACTAM INHIBITOR COMPOUND 31: (2~{S})-5-(2-CHLOROPHENYL)SULFANYL-2-(4-MORPHOLIN-4-YLPHENYL)-4-OXIDANYL-2-THIOPHEN-3-YL-1,3-DIHYDROPYRIDIN-6-ONE
 
Authors :  Z. Chen, C. Eigenbrot
Date :  23 Mar 16  (Deposition) - 14 Sep 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
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  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1GN24Ligand/Ion(2~{S})-5-(2-CHLOROPHENYL)SULFANYL-2-(4-MORPHOLIN-4-YLPHENYL)-4-OXIDANYL-2-THIOPHEN-3-YL-1,3-DIHYDROPYRIDIN-6-ONE
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO47Ligand/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 , LYS A:56 , 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 , LEU A:164 , HIS A:192 , ILE A:251 , GN2 A:404binding site for residue NAD A 401
02AC2SOFTWAREHIS A:185 , ARG C:170 , HIS C:185binding site for residue SO4 A 402
03AC3SOFTWARETRP A:147 , PRO A:153 , LYS A:154binding site for residue SO4 A 403
04AC4SOFTWAREARG A:98 , ASN A:137 , LEU A:164 , ASP A:165 , ARG A:168 , HIS A:192 , GLY A:193 , ALA A:237 , TYR A:238 , ILE A:241 , GLY A:245 , THR A:247 , NAD A:401binding site for residue GN2 A 404
05AC5SOFTWAREGLY B:28 , ALA B:29 , VAL B:30 , ASP B:51 , VAL B:52 , ILE B:53 , THR B:94 , ALA B:95 , GLY B:96 , ARG B:98 , ILE B:115 , ILE B:119 , VAL B:135 , SER B:136 , ASN B:137 , LEU B:164 , HIS B:192 , ILE B:251 , GN2 B:405binding site for residue NAD B 401
06AC6SOFTWAREARG B:170 , HIS B:185 , LEU D:182 , HIS D:185binding site for residue SO4 B 402
07AC7SOFTWAREHIS B:185 , ARG D:170 , HIS D:185binding site for residue SO4 B 403
08AC8SOFTWARELYS A:283 , TRP B:147 , LYS B:154binding site for residue SO4 B 404
09AC9SOFTWAREARG B:98 , ASN B:137 , LEU B:164 , ASP B:165 , ARG B:168 , HIS B:192 , GLY B:193 , ALA B:237 , TYR B:238 , ILE B:241 , THR B:247 , NAD B:401binding site for residue GN2 B 405
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 , ILE C:119 , VAL C:135 , SER C:136 , ASN C:137 , LEU C:164 , HIS C:192 , ILE C:251 , GN2 C:404binding site for residue NAD C 401
11AD2SOFTWAREARG A:170 , HIS A:185 , LEU C:182 , SER C:183 , HIS C:185binding site for residue SO4 C 402
12AD3SOFTWARETRP C:147 , PRO C:153 , LYS C:154binding site for residue SO4 C 403
13AD4SOFTWAREARG 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 , THR C:247 , NAD C:401binding site for residue GN2 C 404
14AD5SOFTWAREGLY 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 , ILE D:115 , PHE D:118 , ILE D:119 , VAL D:135 , SER D:136 , ASN D:137 , LEU D:164 , HIS D:192 , ILE D:251 , GN2 D:402binding site for residue NAD D 401
15AD6SOFTWAREASN D:137 , LEU D:164 , ASP D:165 , ARG D:168 , HIS D:192 , GLY D:193 , ALA D:237 , TYR D:238 , ILE D:241 , GLY D:245 , THR D:247 , NAD D:401binding site for residue GN2 D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IXY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IXY)

(-) 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..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeeeeee..eehhhhh............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ixy 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..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeeeeee..ee................hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ixy 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.....eeeeeee.....eeeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ixy 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheee..........eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.....eeeeee.......eeeeeeeee..eehhhhh...........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeeee...........eeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ixy D   1 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGLNLVQRNVNIFKFIIPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGISDLVKVTLTSEEEARLKKSADTLWGIQKELQF 331
                                    10        20        30        40        50        60        70        80        90       100 ||    113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
                                                                                                                               102|                                                                                                                                                                                                                                 
                                                                                                                                106
   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 '|'

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(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5IXY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        LDHA_HUMAN | P00338: 1i10 4ajp 4jnk 4l4r 4l4s 4m49 4ojn 4okn 4qo7 4qo8 4qsm 4qt0 4r68 4r69 4rls 4zvv 5ixs

(-) Related Entries Specified in the PDB File

5ixs