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(-) Description

Title :  MTB TMK IN COMPLEX WITH COMPOUND 36
 
Authors :  J. A. Read, S. Hussein, H. Gingell, J. Tucker
Date :  30 May 14  (Deposition) - 24 Jun 15  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Transfer (Atp Tmp Phosphotransferase), Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Naik, A. Raichurkar, B. S. Bandodkar, B. V. Varun, S. Bhat, R. Kalkhambkar, K. Murugan, R. Menon, J. Bhat, B. Paul, H. Iyer, S. Hussein, J. A. Tucker, M. Vogtherr, K. J. Embrey, H. Mcmiken, S. Prasad, A. Gill, B. G. Ugarkar, J. Venkatraman, J. Read, M. Panda
Structure Guided Lead Generation For M. Tuberculosis Thymidylate Kinase (Mtb Tmk): Discovery Of 3-Cyanopyridone And 1, 6-Naphthyridin-2-One As Potent Inhibitors.
J. Med. Chem. V. 58 753 2015
PubMed-ID: 25486447  |  Reference-DOI: 10.1021/JM5012947

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1-210
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: THYMIDINE MONOPHOSPHATE KINASE, DTMP KINASE, TMPK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1H6D2Ligand/Ion4-[(R)-METHYLSULFINYL]-2-OXO-6-[3-(TRIFLUOROMETHOXY)PHENYL]-1,2-DIHYDROPYRIDINE-3-CARBONITRILE
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1H6D1Ligand/Ion4-[(R)-METHYLSULFINYL]-2-OXO-6-[3-(TRIFLUOROMETHOXY)PHENYL]-1,2-DIHYDROPYRIDINE-3-CARBONITRILE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1H6D1Ligand/Ion4-[(R)-METHYLSULFINYL]-2-OXO-6-[3-(TRIFLUOROMETHOXY)PHENYL]-1,2-DIHYDROPYRIDINE-3-CARBONITRILE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:37 , TYR A:39 , LEU A:52 , PHE A:70 , ARG A:74 , ARG A:95 , SER A:99 , ASN A:100 , TYR A:103 , SER A:104 , ARG A:107BINDING SITE FOR RESIDUE H6D A1210
2AC2SOFTWAREPRO B:37 , TYR B:39 , LEU B:52 , PHE B:70 , ARG B:74 , ARG B:95 , SER B:99 , ASN B:100 , TYR B:103 , SER B:104 , ARG B:107 , LEU B:171BINDING SITE FOR RESIDUE H6D B1210
3AC3SOFTWAREGLY B:10 , GLY B:12 , LYS B:13BINDING SITE FOR RESIDUE NA B1211

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:36 -Pro A:37
2Phe B:36 -Pro B:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UNQ)

(-) Sequences/Alignments

Asymmetric 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:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh.....hhhhhhhhhhhh.........eeeee.....hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4unq A   1 MLIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFPRYGQSVAADIAAEALHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCRGYDVVILDRYVASNAAYSAARLHENAAGKAAAWVQRIEFARLGLPKPDWQVLLAVSAEDAELQQRTGAVYAELAAQGWGGRWLVVGADVDPGRLAATLAP 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   ||  173       183       193       203      
                                                                                                                                                                         144|                                         
                                                                                                                                                                          168                                         


Chain B from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh.....hhhhhhhhhhhh.........eeeee........hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4unq B   1 MLIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFPRYGQSVAADIAAEALHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCRGYDVVILDRYVASNAAYSAARLHENAAGKAAAWVQRIEFARLGLPKPDWQVLLAVSAELARDAELQQRTGAVYAELAAQGWGGRWLVVGADVDPGRLAATLAP 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     ||170       180       190       200         
                                                                                                                                                                           146|                                          
                                                                                                                                                                            167
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  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 4UNQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KTHY_MYCTU | P9WKE1: 1g3u 1gsi 1gtv 1mrn 1mrs 1n5i 1n5j 1n5k 1n5l 1w2g 1w2h 4unn 4unp 4unr 4uns

(-) Related Entries Specified in the PDB File

4unn MTB TMK IN COMPLEX WITH COMPOUND 8
4unp MTB TMK IN COMPLEX WITH COMPOUND 34
4unr MTB TMK IN COMPLEX WITH COMPOUND 23
4uns MTB TMK IN COMPLEX WITH COMPOUND 40