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(-) Description

Title :  KINASE DOMAIN OF HUMAN EPHB1, G703C MUTANT, COVALENTLY BOUND TO A QUINAZOLINE-BASED INHIBITOR
 
Authors :  A. Kung, M. Schimpl, Y. -C. Chen, R. C. Overman, C. Zhang
Date :  30 Nov 16  (Deposition) - 17 May 17  (Release) - 28 Jun 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 :  Receptor Tyrosine Kinase, Kinase Domain, Inhibitor, Covalent, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kung, M. Schimpl, A. Ekanayake, Y. C. Chen, R. Overman, C. Zhang
A Chemical-Genetic Approach To Generate Selective Covalent Inhibitors Of Protein Kinases.
Acs Chem. Biol. V. 12 1499 2017
PubMed-ID: 28459525  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B01083

(-) Compounds

Molecule 1 - EPHRIN TYPE-B RECEPTOR 1
    Chains: A, B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Gene: EPHB1, ELK, EPHT2, HEK6, NET
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ELK,EPH TYROSINE KINASE 2,EPH-LIKE KINASE 6,HEK6,NEURONALLY- EXPRESSED EPH-RELATED TYROSINE KINASE,NET,TYROSINE-PROTEIN KINASE RECEPTOR EPH-2

 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  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
17O32Ligand/Ion2-CHLORANYL-~{N}-[4-[(2-CHLORANYL-5-OXIDANYL-PHENYL)AMINO]QUINAZOLIN-7-YL]ETHANAMIDE
2PTR4Mod. Amino AcidO-PHOSPHOTYROSINE
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
17O31Ligand/Ion2-CHLORANYL-~{N}-[4-[(2-CHLORANYL-5-OXIDANYL-PHENYL)AMINO]QUINAZOLIN-7-YL]ETHANAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
17O31Ligand/Ion2-CHLORANYL-~{N}-[4-[(2-CHLORANYL-5-OXIDANYL-PHENYL)AMINO]QUINAZOLIN-7-YL]ETHANAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:649 , LYS A:651 , GLU A:668 , THR A:697 , GLU A:698 , PHE A:699 , MET A:700 , CYS A:703 , LEU A:751 , SER A:761 , ASP A:762 , HOH A:1047 , HOH A:1088binding site for residue 7O3 A 901
2AC2SOFTWAREARG A:678 , ARG A:682 , LYS A:759 , HOH A:1013 , HOH A:1045 , HOH A:1076binding site for residue SO4 A 902
3AC3SOFTWARESER A:707 , ARG A:710 , GLN A:711binding site for residue SO4 A 903
4AC4SOFTWAREARG A:748 , TRP A:790 , ARG A:823binding site for residue SO4 A 904
5AC5SOFTWAREARG A:678 , ARG B:678 , ASN B:753 , VAL B:757 , LYS B:759binding site for residue SO4 B 902
6AC6SOFTWARETRP B:790 , ARG B:823 , HOH B:1009 , HOH B:1088binding site for residue SO4 B 903
7AC7SOFTWAREALA B:649 , LYS B:651 , GLU B:668 , THR B:697 , GLU B:698 , MET B:700 , GLU B:701 , ASN B:702 , ALA B:704 , LEU B:751 , VAL B:752 , ASP B:762 , HOH B:1048 , HOH B:1080binding site for Di-peptide 7O3 B 901 and CYS B 703

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:691 -Pro A:692

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MJB)

(-) 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:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh.eeeeeeeee....eeeeeee.......eeeeeee.....hhhhhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mjb A 608 REFAKEIDVSFVKIEEVIGAGEFGEVYKGRLKLPGKREIyVAIKTLKAGYSEKQRRDFLSEASIMGQFDHRNIIRLEGVVTKSRPVMIITEFMENCALDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLSEMNYVHRDLAARNILVNSNLVCKVSDFGLSRYLPTyTSSLGGKIPVRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPMDCPAALHQLMLDCWQKDRNSRPRFAEIVNTLDKMIRNPASLKTV 891
                                   617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767 || |  783       793       803       813       823       833       843       853       863       873       883        
                                                                 647-PTR                                                                                                                   769| |                                                                                                                 
                                                                                                                                                                                            776 |                                                                                                                 
                                                                                                                                                                                              778-PTR                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh.eeeeeeeee....eeeeeee.......eeeeeee.....hhhhhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mjb B 608 REFAKEIDVSFVKIEEVIGAGEFGEVYKGRLKLPGKREIyVAIKTLKAGYSEKQRRDFLSEASIMGQFDHRNIIRLEGVVTKSRPVMIITEFMENCALDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLSEMNYVHRDLAARNILVNSNLVCKVSDFGLSRYLTSDPTyTSSLGGKIPVRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPMDCPAALHQLMLDCWQKDRNSRPRFAEIVNTLDKMIRNPASLKT 890
                                   617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767 ||    780       790       800       810       820       830       840       850       860       870       880       890
                                                                 647-PTR                                                                                                                   769|    |                                                                                                                
                                                                                                                                                                                            773    |                                                                                                                
                                                                                                                                                                                                 778-PTR
   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 5MJB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (55, 55)

Asymmetric Unit(hide GO term definitions)

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    Arg A:691 - Pro A:692   [ RasMol ]  
 
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 Related Entries

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        EPHB1_HUMAN | P54762: 2djs 2eao 3zfx 5mja

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