Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN CREBBP BOUND TO THE BENZODIAZEPINONE G02778174
 
Authors :  H. Jayaram, F. Poy, J. W. Setser, S. F. Bellon
Date :  18 Feb 16  (Deposition) - 20 Apr 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bromodomain Inhibitor, Protein Binding-Inhibitor 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, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: BROMODOMAIN (UNP RESIDUES 1082-1197)
    Gene: CREBBP, CBP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
169A2Ligand/Ion(4R)-N-BENZYL-4-METHYL-2-OXO-2,3,4,5-TETRAHYDRO-1H-1,5-BENZODIAZEPINE-6-CARBOXAMIDE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
169A1Ligand/Ion(4R)-N-BENZYL-4-METHYL-2-OXO-2,3,4,5-TETRAHYDRO-1H-1,5-BENZODIAZEPINE-6-CARBOXAMIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
169A1Ligand/Ion(4R)-N-BENZYL-4-METHYL-2-OXO-2,3,4,5-TETRAHYDRO-1H-1,5-BENZODIAZEPINE-6-CARBOXAMIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3SCN-1Ligand/IonTHIOCYANATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:1098 , TYR A:1102 , LEU A:1135 , SER A:1136 , HOH A:1314 , HOH A:1417binding site for residue SCN A 1202
2AC2SOFTWAREPRO A:1110 , LEU A:1120 , TYR A:1125 , ASN A:1168 , ARG A:1173 , VAL A:1174 , HOH A:1309 , HOH A:1350binding site for residue 69A A 1203
3AC3SOFTWAREPRO B:1110 , VAL B:1115 , LEU B:1120 , TYR B:1125 , ASN B:1168 , ARG B:1173 , VAL B:1174 , HOH B:1306 , HOH B:1316binding site for residue 69A B 1202
4AC4SOFTWAREASN A:1168 , SER A:1172 , ARG A:1173 , VAL A:1174 , HOH A:1353 , GLU B:1186binding site for residues EDO A 1201 and EDO B 1201
5AC5SOFTWAREASN A:1168 , SER A:1172 , ARG A:1173 , VAL A:1174 , HOH A:1353 , GLU B:1186binding site for residues EDO A 1201 and EDO B 1201
6AC6SOFTWAREASN A:1168 , SER A:1172 , ARG A:1173 , VAL A:1174 , HOH A:1353 , GLU B:1186binding site for residues EDO A 1201 and EDO B 1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I86)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:1105 -Pro A:1106
2Asp B:1105 -Pro B:1106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I86)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I86)

(-) Exons   (0, 0)

(no "Exon" information available for 5I86)

(-) 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:115
                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh....hhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                5i86 A 1082 KKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 1196
                                  1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191     


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh....hhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                5i86 B 1083 KIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL 1196
                                  1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192
   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 5I86)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I86)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I86)

(-) Gene Ontology  (66, 66)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    69A  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SCN  [ 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 ]
 
  Cis Peptide Bonds
    Asp A:1105 - Pro A:1106   [ RasMol ]  
    Asp B:1105 - Pro B:1106   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5i86
    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)
  (no 'Enzyme Classificator' available)
    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 5i89 5i8b 5i8g 5j0d 5jem 5ktu 5ktw 5ktx 5mpz 5mqe 5mqg 5mqk 5tb6

(-) Related Entries Specified in the PDB File

5i83 5i89