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(-) Description

Title :  KINASE DOMAIN OF HUMAN EPHB1 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 :  2.14
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Receptor Tyrosine Kinase, Kinase Domain, Inhibitor, 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: 562
    Expression System Variant: GOLD
    Gene: EPHB1, ELK, EPHT2, HEK6, NET
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: PHOSPHORYLATION ON TYR647 AND TYR778 AS A RESULT OF AUTOPHOSPHORYLATION DURING RECOMBINANT EXPRESSION IN E.COLI
    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, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
17O32Ligand/Ion2-CHLORANYL-~{N}-[4-[(2-CHLORANYL-5-OXIDANYL-PHENYL)AMINO]QUINAZOLIN-7-YL]ETHANAMIDE
2PTR4Mod. Amino AcidO-PHOSPHOTYROSINE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
17O31Ligand/Ion2-CHLORANYL-~{N}-[4-[(2-CHLORANYL-5-OXIDANYL-PHENYL)AMINO]QUINAZOLIN-7-YL]ETHANAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
17O31Ligand/Ion2-CHLORANYL-~{N}-[4-[(2-CHLORANYL-5-OXIDANYL-PHENYL)AMINO]QUINAZOLIN-7-YL]ETHANAMIDE
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:633 , ALA A:649 , LYS A:651 , GLU A:668 , THR A:697 , GLU A:698 , MET A:700 , GLY A:703 , LEU A:751 , SER A:761 , ASP A:762 , HOH A:1044binding site for residue 7O3 A 901
2AC2SOFTWAREASP A:879 , ARG A:883 , HOH A:1030 , LYS B:643binding site for residue SO4 A 902
3AC3SOFTWAREALA B:649 , LYS B:651 , GLU B:668 , THR B:697 , GLU B:698 , MET B:700 , GLU B:701 , GLY B:703 , LEU B:751 , SER B:761 , ASP B:762 , HOH B:1091 , HOH B:1136binding site for residue 7O3 B 901
4AC4SOFTWAREARG A:682 , GLU A:698 , LYS A:759 , ARG B:678 , HOH B:1102binding site for residue SO4 B 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:691 -Pro A:692
2Arg B:691 -Pro B:692

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MJA)

(-) 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:273
                                                                                                                                                                                                                                                                                                                 
               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
                 5mja A 609 EFAKEIDVSFVKIEEVIGAGEFGEVYKGRLKLPGKREIyVAIKTLKAGYSEKQRRDFLSEASIMGQFDHRNIIRLEGVVTKSRPVMIITEFMENGALDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLSEMNYVHRDLAARNILVNSNLVCKVSDFGLSRYLPTyTSSPVRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPMDCPAALHQLMLDCWQKDRNSRPRFAEIVNTLDKMIRNPASLKTVA 892
                                   618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768|| |  |789       799       809       819       829       839       849       859       869       879       889   
                                                                647-PTR                                                                                                                   769| |  ||                                                                                                         
                                                                                                                                                                                           776 |  ||                                                                                                         
                                                                                                                                                                                             778-PTR                                                                                                         
                                                                                                                                                                                                781|                                                                                                         
                                                                                                                                                                                                 787                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhh.eeeeeeeee....eeeeeee.......eeeeeee.....hhhhhhhhhhhhhhhh.........eeeee......eeeee....eehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mja B 609 EFAKEIDVSFVKIEEVIGAGEFGEVYKGRLKLPGKREIyVAIKTLKAGYSEKQRRDFLSEASIMGQFDHRNIIRLEGVVTKSRPVMIITEFMENGALDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLSEMNYVHRDLAARNILVNSNLVCKVSDFGLSRYLPTyTSSLGGKIPVRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPMDCPAALHQLMLDCWQKDRNSRPRFAEIVNTLDKMIRNPASLKT 890
                                   618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768|| |   784       794       804       814       824       834       844       854       864       874       884      
                                                                647-PTR                                                                                                                   769| |                                                                                                                
                                                                                                                                                                                           776 |                                                                                                                
                                                                                                                                                                                             778-PTR
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 5MJA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (55, 55)

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  5mja
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  EPHB1_HUMAN | P54762
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  2.7.10.1
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 Related Entries

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UniProtKB/Swiss-Prot
        EPHB1_HUMAN | P54762: 2djs 2eao 3zfx 5mjb

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