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 :  DISCOVERY AND STRUCTURE-ACTIVITY RELATIONSHIPS OF A HIGHLY SELECTIVE BUTYRYLCHOLINESTERASE INHIBITOR BY STRUCTURE-BASED VIRTUAL SCREENING
 
Authors :  E. De La Mora, S. N. Dighe, G. S. Deora, B. P. Ross, F. Nachon, X. Brazzol
Date :  23 May 16  (Deposition) - 27 Jul 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  High Selective Inhibitor, Butyrylcholinesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Dighe, G. S. Deora, E. De La Mora, F. Nachon, S. Chan, M. O. Parat, X. Brazzolotto, B. P. Ross
Discovery And Structure-Activity Relationships Of A Highly Selective Butyrylcholinesterase Inhibitor By Structure-Base Virtual Screening.
J. Med. Chem. V. 59 7683 2016
PubMed-ID: 27405689  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00356

(-) Compounds

Molecule 1 - CHOLINESTERASE
    Chains: A, B
    EC Number: 3.1.1.8
    Engineered: YES
    Expression System: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    Gene: BCHE, CHE1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ACYLCHOLINE ACYLHYDROLASE,BUTYRYLCHOLINE ESTERASE,CHOLINE ESTERASE II,PSEUDOCHOLINESTERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 23)

Asymmetric/Biological Unit (4, 23)
No.NameCountTypeFull Name
16QS2Ligand/Ion[(2~{R})-OXOLAN-2-YL]METHYL 4-(9-ETHYLCARBAZOL-3-YL)-2-METHYL-5-OXIDANYLIDENE-4,6,7,8-TETRAHYDRO-1~{H}-QUINOLINE-3-CARBOXYLATE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:14 , ASN A:57binding site for residue NAG A 602
02AC2SOFTWARETRP A:82 , GLY A:115 , GLY A:116 , GLY A:117 , GLU A:197 , SER A:198 , PRO A:285 , SER A:287 , ALA A:328 , PHE A:398 , HIS A:438 , HOH A:701 , HOH A:731 , HOH A:749binding site for residue 6QS A 609
03AC3SOFTWARETYR A:396 , PRO A:401binding site for residue EDO A 610
04AC4SOFTWAREARG B:14 , ASN B:57binding site for residue NAG B 602
05AC5SOFTWARETRP B:82 , GLY B:115 , GLY B:116 , GLY B:117 , GLU B:197 , SER B:198 , PRO B:285 , SER B:287 , ALA B:328 , PHE B:329 , TYR B:332 , HIS B:438binding site for residue 6QS B 609
06AC6SOFTWAREHIS B:77 , GLU B:443binding site for residue EDO B 610
07AC7SOFTWAREASN B:245 , PHE B:278binding site for residue EDO B 611
08AC8SOFTWARETYR B:61 , TRP B:98 , ASP B:129 , LYS B:131binding site for residue GOL B 612
09AC9SOFTWAREGLU A:411 , TRP A:412 , LYS B:248 , GLY B:251 , SER B:253binding site for residue GOL B 613
10AD1SOFTWAREILE A:4 , ASN A:17 , THR A:24binding site for Mono-Saccharide NAG A 601 bound to ASN A 17
11AD2SOFTWAREASN A:106 , ASN A:188binding site for Poly-Saccharide residues NAG A 603 through NAG A 604 bound to ASN A 106
12AD3SOFTWAREGLU A:238 , ASN A:241 , ASN A:245binding site for Mono-Saccharide NAG A 605 bound to ASN A 241
13AD4SOFTWARESER A:338 , ASN A:341binding site for Mono-Saccharide NAG A 606 bound to ASN A 341
14AD5SOFTWAREASN A:473 , TYR A:477 , ASN A:481 , GLU A:482 , ASP B:87 , LEU B:88 , GLN B:270binding site for Poly-Saccharide residues NAG A 607 through NAG A 608 bound to ASN A 481
15AD6SOFTWAREILE B:4 , ASN B:17 , THR B:24binding site for Mono-Saccharide NAG B 601 bound to ASN B 17
16AD7SOFTWAREASN B:106 , ASN B:188binding site for Mono-Saccharide NAG B 603 bound to ASN B 106
17AD8SOFTWAREASN B:241 , ASN B:245 , PRO B:281binding site for Mono-Saccharide NAG B 604 bound to ASN B 241
18AD9SOFTWAREASN B:256binding site for Mono-Saccharide NAG B 605 bound to ASN B 256
19AE1SOFTWAREGLY B:336 , SER B:338 , ASN B:341binding site for Poly-Saccharide residues NAG B 606 through NAG B 607 bound to ASN B 341
20AE2SOFTWAREASN B:481 , GLU B:482 , THR B:483binding site for Mono-Saccharide NAG B 608 bound to ASN B 481

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:65 -A:92
2A:252 -A:263
3A:400 -A:519
4B:65 -B:92
5B:252 -B:263
6B:400 -B:519

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:101 -Pro A:102
2Ala B:101 -Pro B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K5E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K5E)

(-) Exons   (0, 0)

(no "Exon" information available for 5K5E)

(-) 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:527
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.eeeee..eeeeeeeeee.....hhhhh............eee..................hhhhhh............eeeeeee......eeeeeee...........hhhhhhhhhhhhhh.eeeee...hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhh.....................hhhhhhhhh......eeeeee...hhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....................eeeee......eee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k5e A   3 DIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV 529
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       


Chain B from PDB  Type:PROTEIN  Length:526
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.eeeee..eeeeeeeeee.....hhhhh.............ee......ee..........hhhhhh......ee....eeeeeee......eeeeeee...........hhhhhhhhhhhhhh.eeeee....hhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhh.hhhhhhhh.eeeee...........hhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhh........................hhhhhhhhh......eeeeee...hhhhhhh.............hhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....................eeeee......eee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k5e B   4 IIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV 529
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523
   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 ; only for superseded entry 4AQD: 1,2)

(no "SCOP Domain" information available for 5K5E, only for superseded entry 4AQD replaced by 5K5E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K5E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K5E)

(-) Gene Ontology  (28, 28)

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
    6QS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ 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 ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
    AE1  [ RasMol ]  +environment [ RasMol ]
    AE2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:101 - Pro A:102   [ RasMol ]  
    Ala B:101 - Pro B:102   [ 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
  5k5e
    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
  CHLE_HUMAN | P06276
    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)
  3.1.1.8
    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
  CHLE_HUMAN | P06276
    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
        CHLE_HUMAN | P06276: 1eho 1ehq 1kcj 1p0i 1p0m 1p0p 1p0q 1xlu 1xlv 1xlw 2j4c 2pm8 2wid 2wif 2wig 2wij 2wik 2wil 2wsl 2xmb 2xmc 2xmd 2xmg 2xqf 2xqg 2xqi 2xqj 2xqk 2y1k 3djy 3dkk 3o9m 4aqd 4axb 4b0o 4b0p 4bbz 4bds 4tpk 4xii 5dyt 5dyw 5dyy 5lkr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5K5E)