Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CBP IN COMPLEX WITH CPD637 ((R)-4-METHYL-6-(1-METHYL-3-(1-METHYL-1H-PYRAZOL-4-YL)-1H-INDAZOL-5-YL)-1,3,4,5-TETRAHYDRO-2H-BENZO[B][1, 4]DIAZEPIN-2-ONE)
 
Authors :  J. M. Murray
Date :  18 Feb 16  (Deposition) - 20 Apr 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym./Biol. Unit :  A
Keywords :  Crebbp, Bromodomain, Epigenetics, Structure-Based Drug Design, Transcription-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Taylor, A. Cote, M. C. Hewitt, R. Pastor, Y. Leblanc, C. G. Nasveschuk, F. A. Romero, T. D. Crawford, N. Cantone, H. Jayaram, J. Setser, J. Murray, M. H. Beresini, G. De Leon Boenig, Z. Chen, A. R. Conery, R. T. Cummings, L. A. Dakin, E. M. Flynn, O. W. Huang, S. Kaufman, P. J. Keller, J. R. Kiefer, T. Lai, Y. Li, J. Liao, W. Liu, H. Lu, E. Pardo, V. Tsui, J. Wang, Y. Wang, Z. Xu, F. Yan, D. Yu, L. Zawadzke, X. Zhu, X. Zhu, R. J. Sims, A. G. Cochran, S. Bellon, J. E. Audia, S. Magnuson, B. K. Albrecht
Fragment-Based Discovery Of A Selective And Cell-Active Benzodiazepinone Cbp/Ep300 Bromodomain Inhibitor (Cpi-637).
Acs Med. Chem. Lett. V. 7 531 2016
PubMed-ID: 27190605  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00075

(-) Compounds

Molecule 1 - CREB-BINDING PROTEIN
    Chains: A
    EC Number: 2.3.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CREBBP, CBP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
169E1Ligand/Ion(4R)-4-METHYL-6-[1-METHYL-3-(1-METHYL-1H-PYRAZOL-4-YL)-1H-INDAZOL-5-YL]-1,3,4,5-TETRAHYDRO-2H-1,5-BENZODIAZEPIN-2-ONE
2B3P1Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3EDO5Ligand/Ion1,2-ETHANEDIOL
4NA1Ligand/IonSODIUM ION
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
6ZN3Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:1199 , CYS A:1200 , HIS A:1291 , CYS A:1294binding site for residue ZN A 1401
02AC2SOFTWARECYS A:1283 , CYS A:1286 , CYS A:1308 , CYS A:1311binding site for residue ZN A 1402
03AC3SOFTWARECYS A:1213 , CYS A:1219 , CYS A:1237 , CYS A:1240binding site for residue ZN A 1403
04AC4SOFTWARELEU A:1109 , PRO A:1110 , GLN A:1113 , VAL A:1115 , LEU A:1120 , TYR A:1125 , TYR A:1167 , ASN A:1168 , ARG A:1173 , VAL A:1174 , PEG A:1412 , HOH A:1534 , HOH A:1621binding site for residue 69E A 1404
05AC5SOFTWAREASN A:1162 , TRP A:1165 , TYR A:1204 , ASP A:1273 , THR A:1274 , LEU A:1275 , EDO A:1407 , HOH A:1569 , HOH A:1600binding site for residue B3P A 1405
06AC6SOFTWARELYS A:1141 , GLN A:1146 , GLN A:1152 , HOH A:1559binding site for residue EDO A 1406
07AC7SOFTWARETRP A:1165 , TYR A:1175 , SER A:1179 , B3P A:1405binding site for residue EDO A 1407
08AC8SOFTWAREVAL A:1281 , GLY A:1305 , PHE A:1306 , HOH A:1516binding site for residue EDO A 1408
09AC9SOFTWAREPRO A:1087 , GLU A:1088 , ARG A:1091 , LEU A:1142 , ASP A:1143 , GLY A:1145 , HOH A:1664binding site for residue EDO A 1409
10AD1SOFTWARELYS A:1176 , HIS A:1297 , TYR A:1298 , ASP A:1299 , HOH A:1501 , HOH A:1596binding site for residue EDO A 1410
11AD2SOFTWAREARG A:1173 , LYS A:1176 , TYR A:1298binding site for residue NA A 1411
12AD3SOFTWARE69E A:1404binding site for residue PEG A 1412
13AD4SOFTWARELEU A:1098 , GLU A:1099 , TYR A:1102 , LEU A:1135 , LYS A:1139 , HOH A:1515 , HOH A:1531binding site for residue PEG A 1413

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I8G)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:1105 -Pro A:1106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I8G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I8G)

(-) Exons   (0, 0)

(no "Exon" information available for 5I8G)

(-) 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:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh....hhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..............ee.......ee....eeeee...eeee......................eeee........eee......eeehhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5i8g A 1079 GSRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLGYCCGRKYEFSPQTLCCYGKQLCTIPRDAAYYSYQNRYHFCEKCFTLGDDPSQPQTTISKDQFEKKKNDTLDPEPFVDCKECGRKMHQICVLHYDIIWPSGFVCDNCL 1312
                                  1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238  ||  1256      1266      1276      1286      1296      1306      
                                                                                                                                                                                           1241|                                                              
                                                                                                                                                                                            1250
   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 5I8G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I8G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I8G)

(-) Gene Ontology  (66, 66)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    69E  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    B3P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:1105 - Pro A:1106   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5i8g
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CBP_HUMAN | Q92793
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.3.1.48
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CBP_HUMAN | Q92793
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CBP_HUMAN | Q92793: 1jsp 1liq 1rdt 1wo3 1wo4 1wo5 1wo6 1wo7 1zoq 2d82 2kje 2kwf 2l84 2l85 2lxs 2lxt 2n1a 2rny 3dwy 3p1c 3p1d 3p1e 3p1f 3svh 4a9k 4n3w 4n4f 4nr4 4nr5 4nr6 4nr7 4nyv 4nyw 4nyx 4ouf 4tqn 4ts8 4whu 4yk0 5cgp 5dbm 5eic 5eng 5ep7 5gh9 5h85 5i83 5i86 5i89 5i8b 5j0d 5jem 5ktu 5ktw 5ktx 5mpz 5mqe 5mqg 5mqk 5tb6

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5I8G)