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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EGFR KINASE DOMAIN (L858R, T790M, V948R) IN COMPLEX WITH 4-(4-{[2-{[(3S)-1-ACETYLPYRROLIDIN-3-YL]AMINO}-9-(PROPAN-2-YL)-9H-PURIN-6-YL]AMINO}PHENYL)-1-METHYLPIPERAZIN-1-IUM
 
Authors :  K. S. Gajiwala, R. A. Ferre
Date :  07 Jan 17  (Deposition) - 22 Mar 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Covalent Inhibitor, Lung Cancer, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Planken, D. C. Behenna, S. K. Nair, T. O. Johnson, A. Nagata, C. Almaden, S. Bailey, T. E. Ballard, L. Bernier, H. Cheng, S. Cho-Schultz, D. Dalvie, J. G. Deal, D. M. Dinh, M. P. Edwards, R. A. Ferre, K. S. Gajiwala, M. Hemkens, R. S. Kania, J. C. Kath, J. Matthews, B. W. Murray, S. Niessen, S. T. Orr, M. Pairish, N. W. Sach, H. Shen, M. Shi, J. Solowiej, K. Tran, E. Tseng, P. Vicini, Y. Wang, S. L. Weinrich, R. Zhou, M. Zientek, L. Liu, Y. Luo, S. Xin, C. Zhang, J. Lafontaine
Discovery Of N-((3R, 4R)-4-Fluoro-1-(6-((3-Methoxy-1-Methyl-1H-Pyrazol-4- L)Amino)-9-Methyl-9H-Purin-2-Yl)Pyrrolidine-3-Yl)Acrylamide (Pf-06747775) Through Structure-Based Drug Design: A High Affinity Irreversible Inhibitor Targeting Oncogenic Egfr Mutants With Selectivity Over Wild-Type Egfr.
J. Med. Chem. V. 60 3002 2017
PubMed-ID: 28287730  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01894

(-) Compounds

Molecule 1 - EPIDERMAL GROWTH FACTOR RECEPTOR
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA AFF. FRUGIPERDA 2 RZ-2014
    Expression System Taxid: 1491790
    Fragment: UNP RESIDUES 695-1022
    Gene: EGFR, ERBB, ERBB1, HER1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTO-ONCOGENE C-ERBB-1,RECEPTOR TYROSINE-PROTEIN KINASE ERBB-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
18BM1Ligand/Ion4-(4-{[2-{[(3S)-1-ACETYLPYRROLIDIN-3-YL]AMINO}-9-(PROPAN-2-YL)-9H-PURIN-6-YL]AMINO}PHENYL)-1-METHYLPIPERAZIN-1-IUM
2GOL3Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:718 , GLY A:719 , SER A:720 , VAL A:726 , ALA A:743 , GLN A:791 , MET A:793 , PRO A:794 , GLY A:796 , ASN A:842 , LEU A:844 , THR A:854binding site for residue 8BM A 9001
2AC2SOFTWAREARG A:836 , TYR A:869 , ALA A:871 , GLU A:872 , GLY A:873 , HOH A:9113 , HOH A:9182binding site for residue SO4 A 9002
3AC3SOFTWAREARG A:803 , LYS A:913 , HOH A:9131binding site for residue SO4 A 9003
4AC4SOFTWARESER A:752 , ASN A:816 , GLN A:820 , LYS A:823 , HOH A:9102binding site for residue GOL A 9004
5AC5SOFTWARETHR A:940 , ILE A:941 , ASP A:942 , ARG A:977 , TYR A:978 , HOH A:9121 , HOH A:9162 , HOH A:9188binding site for residue GOL A 9005
6AC6SOFTWARELEU A:747 , ALA A:750 , PRO A:753 , LYS A:754binding site for residue GOL A 9006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UGA)

(-) 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:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeeeeeeeee..eeeeeeee........eeeeeeee.......hhhhhhhhhhhhhh........eeeeee...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee.......ee......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uga A 703 LLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDE 985
                                   712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982
   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 5UGA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (111, 111)

Asymmetric/Biological Unit(hide GO term definitions)

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  5uga
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 Related Entries

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

UniProtKB/Swiss-Prot
        EGFR_HUMAN | P00533: 1dnq 1dnr 1ivo 1m14 1m17 1mox 1nql 1xkk 1yy9 1z9i 2eb2 2eb3 2exp 2exq 2gs2 2gs6 2gs7 2itn 2ito 2itp 2itq 2itt 2itu 2itv 2itw 2itx 2ity 2itz 2j5e 2j5f 2j6m 2jit 2jiu 2jiv 2ks1 2m0b 2m20 2n5s 2rf9 2rfd 2rfe 2rgp 3b2u 3b2v 3bel 3buo 3c09 3g5v 3g5y 3gop 3gt8 3ika 3lzb 3njp 3ob2 3op0 3p0y 3pfv 3poz 3qwq 3ug1 3ug2 3vjn 3vjo 3vrp 3vrr 3w2o 3w2p 3w2q 3w2r 3w2s 3w32 3w33 4g5j 4g5p 4hjo 4i1z 4i20 4i21 4i22 4i23 4i24 4jq7 4jq8 4jr3 4jrv 4krl 4krm 4kro 4krp 4li5 4ll0 4lqm 4lrm 4r3p 4r3r 4r5s 4riw 4rix 4riy 4rj4 4rj5 4rj6 4rj7 4rj8 4tks 4uip 4uv7 4wd5 4wkq 4wrg 4zau 4zjv 4zse 5c8k 5c8m 5c8n 5cal 5can 5cao 5cap 5caq 5cas 5cau 5cav 5cnn 5cno 5czh 5czi 5d41 5edp 5edq 5edr 5em5 5em6 5em7 5em8 5fed 5fee 5feq 5gmp 5gnk 5hcx 5hcy 5hcz 5hg5 5hg7 5hg8 5hg9 5hib 5hic 5j9y 5j9z 5jeb 5lv6 5sx4 5sx5 5u8l 5ug8 5ug9 5ugb 5ugc

(-) Related Entries Specified in the PDB File

5ug8 5ug9 5ugb 5ugc