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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE PROTO-ONCOGENE TYROSINE-PROTEIN KINASE MER IN COMPLEX WITH INHIBITOR UNC2541
 
Authors :  A. L. Mciver, W. Zhang, Q. Liu, X. Jiang, M. A. Stashko, J. Nichols, M. J. M J. Norris-Drouin, M. Machius, D. Deryckere, E. Wood, D. K. Graham, H. S D. Kireev, S. V. Frye, X. Wang
Date :  17 May 16  (Deposition) - 22 Feb 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Macrocyclic, Drug Design, Fibrinolytic Agents, Protein Kinase Inhibitors, Proto-Oncogene Proteins, Pyrimidines, Receptor Protein- Tyrosine Kinases, Structure-Activity Relationship, Thrombosis, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Mciver, W. Zhang, Q. Liu, X. Jiang, M. A. Stashko, J. Nichols, M. J. Miley, J. Norris-Drouin, M. Machius, D. Deryckere, E. Wood, D. K. Graham, H. S. Earp, D. Kireev, S. V. Frye, X. Wang
Discovery Of Macrocyclic Pyrimidines As Mertk-Specific Inhibitors.
Chemmedchem V. 12 207 2017
PubMed-ID: 28032464  |  Reference-DOI: 10.1002/CMDC.201600589

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE MER
    Chains: A, B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 570-864
    Gene: MERTK, MER
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTO-ONCOGENE C-MER,RECEPTOR TYROSINE KINASE MERTK

 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, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2K0X2Ligand/Ion(7S)-7-AMINO-N-[(4-FLUOROPHENYL)METHYL]-8-OXO-2,9,16,18,21-PENTAAZABICYCLO[15.3.1]HENICOSA-1(21),17,19-TRIENE-20-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K0X1Ligand/Ion(7S)-7-AMINO-N-[(4-FLUOROPHENYL)METHYL]-8-OXO-2,9,16,18,21-PENTAAZABICYCLO[15.3.1]HENICOSA-1(21),17,19-TRIENE-20-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K0X1Ligand/Ion(7S)-7-AMINO-N-[(4-FLUOROPHENYL)METHYL]-8-OXO-2,9,16,18,21-PENTAAZABICYCLO[15.3.1]HENICOSA-1(21),17,19-TRIENE-20-CARBOXAMIDE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:584 , LEU A:589binding site for residue CL A 901
2AC2SOFTWAREPRO A:802 , LYS A:820binding site for residue CL A 902
3AC3SOFTWAREARG A:687 , MET B:798 , HOH B:1036binding site for residue CL A 903
4AC4SOFTWARELEU A:593 , ALA A:617 , PRO A:672 , PHE A:673 , MET A:674 , LYS A:675 , ARG A:727 , ASN A:728 , MET A:730 , ASP A:741binding site for residue K0X A 904
5AC5SOFTWAREPRO B:802 , LYS B:820 , HOH B:1016binding site for residue CL B 901
6AC6SOFTWAREARG B:584 , LEU B:587 , ILE B:588 , LEU B:589binding site for residue CL B 902
7AC7SOFTWARELEU B:593 , ALA B:617 , PRO B:672 , MET B:674 , LYS B:675 , ARG B:727 , ASN B:728 , MET B:730binding site for residue K0X B 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K0X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K0X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K0X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K0X)

(-) Exons   (0, 0)

(no "Exon" information available for 5K0X)

(-) 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:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhh.eeeeeeee...eeeeeee.....eeeeeeee.............hhhhhhhh..........eeee...eeeeee.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k0x A 576 KLEDVVIDRNLLILGKILGEGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQIEEFLSEAACMKDFSHPNVIRLLGVCIEPKPMVILPFMKYGDLHTYLLYSRLETGPKHIPLQTLLKFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLEKLLESLPD 863
                                   585       595|      608       618       628|      640       650       666       676       686       696       706       716       726       736      |765       775       785       795       805       815       825       835       845       855        
                                             595|                          628|                        658|                                                                           743|                                                                                                    
                                              599                           631                         665                                                                            763                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...hhh.eeeeeeee....eeeeeee.....eeeeeee..hhhhhhhhhhh.........eeeeee.....eeeeeeee.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k0x B 575 NKLEDVVIDRNLLILGKILGEFGSVMEGNLKQEDGTSLKVAVKTEFLSEAACMKDFSHPNVIRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPKHIPLQTLLKFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLEKLLESLPD 863
                                   584       594||     606       616   ||  638       648       658       668       678       688       698       708       718       728       738  ||   769       779       789       799       809       819       829       839       849       859    
                                              595|                   620|                                                                                                         741|                                                                                                    
                                               598                    633                                                                                                          763
   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  (0, 0)

(no "SCOP Domain" information available for 5K0X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K0X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K0X)

(-) Gene Ontology  (35, 35)

Asymmetric Unit(hide GO term definitions)

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  5k0x
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  MERTK_HUMAN | Q12866
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 Related Entries

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

UniProtKB/Swiss-Prot
        MERTK_HUMAN | Q12866: 2dbj 2p0c 3bpr 3brb 3tcp 4m3q 4mh7 4mha 5k0k 5tc0 5td2

(-) Related Entries Specified in the PDB File

5k0k