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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN BUTYRYLCHOLINESTERASE IN COMPLEX WITH N-((1-BENZYLPIPERIDIN-3-YL)METHYL)-N-(2-METHOXYETHYL)NAPHTHALENE-2-SULFONAMIDE
 
Authors :  N. Coquelle, B. Brus, J. P. Colletier
Date :  25 Sep 15  (Deposition) - 18 Jan 17  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Human Butyrylcholinesterase Ad Alzheimer Disease Sulfonamide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Kosak, B. Brus, D. Knez, R. Sink, S. Zakelj, J. Trontelj, A. Pislar, J. Slenc, M. Gobec, M. Zivin, L. Tratnjek, M. Perse, K. Saat, A. Podkowa B. Filipek, F. Nachon, X. Brazzolotto, A. Wieckowska, B. Malawska, J. Stojan, I. M. Rascan, J. Kos, N. Coquelle, J. P. Colletier, S. Gobec
Development Of An In-Vivo Active Reversible Butyrylcholinesterase Inhibitor.
Sci Rep V. 6 39495 2016
PubMed-ID: 28000737  |  Reference-DOI: 10.1038/SREP39495

(-) Compounds

Molecule 1 - CHOLINESTERASE
    Chains: A, B
    EC Number: 3.1.1.8
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Common: FRUIT FLY
    Expression System Taxid: 7227
    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  (8, 55)

Asymmetric/Biological Unit (8, 55)
No.NameCountTypeFull Name
15HF2Ligand/IonN-{[(3S)-1-BENZYLPIPERIDIN-3-YL]METHYL}-N-(2-METHOXYETHYL)NAPHTHALENE-2-SULFONAMIDE
2CL4Ligand/IonCHLORIDE ION
3EDO9Ligand/Ion1,2-ETHANEDIOL
4FUC2Ligand/IonALPHA-L-FUCOSE
5FUL4Ligand/IonBETA-L-FUCOSE
6GOL9Ligand/IonGLYCEROL
7NAG24Ligand/IonN-ACETYL-D-GLUCOSAMINE
8PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (40, 40)

Asymmetric Unit (40, 40)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:68 , GLY A:116 , GLY A:117 , GLN A:119 , THR A:120 , SER A:198 , TRP A:231 , SER A:287 , PHE A:398 , TRP A:430 , MET A:437 , HIS A:438binding site for residue 5HF A 601
02AC2SOFTWARELEU A:18 , TYR A:61 , TRP A:98 , ASP A:129 , LYS A:131binding site for residue GOL A 602
03AC3SOFTWAREPRO A:189 , LYS A:190 , SER A:215 , PHE A:217 , THR A:218 , LYS A:313binding site for residue GOL A 603
04AC4SOFTWARETYR A:396 , CYS A:400 , PRO A:401 , TRP A:522 , THR A:523binding site for residue GOL A 604
05AC5SOFTWARETYR A:33 , SER A:48 , LEU A:49 , TRP A:177 , LYS A:180binding site for residue GOL A 605
06AC6SOFTWAREASN A:479 , TRP A:490 , HOH A:759 , GLN B:71binding site for residue EDO A 606
07AC7SOFTWARETHR A:108 , ASN A:188binding site for residue EDO A 607
08AC8SOFTWAREHIS A:77 , LYS A:427 , GLU A:443binding site for residue EDO A 608
09AC9SOFTWARELYS A:494 , SER A:495 , THR A:496binding site for residue EDO A 609
10AD1SOFTWAREARG A:386 , GLU A:387 , TRP A:433binding site for residue EDO A 610
11AD2SOFTWARELEU A:29 , GLY A:30 , TRP A:56 , ASN A:57 , LYS A:60 , ALA A:62 , TYR A:94 , HOH A:777binding site for residue EDO A 611
12AD3SOFTWAREARG A:386binding site for residue CL A 612
13AD4SOFTWAREGLU A:197binding site for residue CL A 613
14AD5SOFTWARESER A:426 , ASN A:455 , TYR A:456 , NAG A:616binding site for residue PG4 A 614
15AD6SOFTWAREASN B:68 , ILE B:69 , ASP B:70 , TRP B:82 , GLY B:116 , GLY B:117 , GLN B:119 , THR B:120 , SER B:198 , SER B:287 , ALA B:328 , PHE B:329 , PHE B:398 , TRP B:430 , MET B:437 , HIS B:438binding site for residue 5HF B 601
16AD7SOFTWARELEU B:18 , TYR B:61 , TRP B:98 , ASP B:129 , LYS B:131binding site for residue GOL B 602
17AD8SOFTWAREARG B:240 , LEU B:244 , GLU B:255 , GLU B:411 , TRP B:412 , GLY B:413binding site for residue GOL B 603
18AD9SOFTWAREPRO B:46 , GLN B:47 , SER B:48binding site for residue GOL B 604
19AE1SOFTWARETRP B:231 , THR B:284 , LEU B:286 , SER B:287 , ASN B:397binding site for residue GOL B 605
20AE2SOFTWAREPRO B:449 , GLU B:451 , ARG B:452 , ASP B:454 , ASN B:455 , TYR B:456 , GLU B:461binding site for residue GOL B 606
21AE3SOFTWAREARG B:42 , LYS B:267binding site for residue EDO B 607
22AE4SOFTWARELYS A:528 , ARG B:347 , GLN B:351 , GLU B:367binding site for residue EDO B 608
23AE5SOFTWAREHIS B:77 , GLU B:443binding site for residue EDO B 609
24AE6SOFTWAREARG B:242 , VAL B:288binding site for residue CL B 610
25AE7SOFTWAREGLU B:197binding site for residue CL B 611
26AE8SOFTWAREASN A:17 , THR A:24 , PG4 A:614 , HOH A:764binding site for Poly-Saccharide residues NAG A 615 through NAG A 616 bound to ASN A 17
27AE9SOFTWAREARG A:14 , ILE A:55 , ASN A:57 , LYS B:12binding site for Poly-Saccharide residues NAG A 617 through FUC A 619 bound to ASN A 57
28AF1SOFTWAREASN A:106 , ASN A:188 , LYS A:190binding site for Poly-Saccharide residues NAG A 620 through NAG A 621 bound to ASN A 106
29AF2SOFTWAREASN A:241 , ASN A:245 , LYS A:248 , PHE A:278 , VAL A:280 , PRO A:281 , NAG B:622 , NAG B:623 , FUL B:624binding site for Poly-Saccharide residues NAG A 622 through FUC A 624 bound to ASN A 241
30AF3SOFTWARESER A:338 , ASN A:341 , HOH A:702 , HOH A:727 , HOH A:799binding site for Mono-Saccharide NAG A 625 bound to ASN A 341
31AF4SOFTWARETYR A:477 , ASN A:479 , ASN A:481 , GLU A:482 , THR A:483 , GLN A:484 , ASP B:87 , LEU B:88 , GLN B:270binding site for Poly-Saccharide residues NAG A 626 through NAG A 627 bound to ASN A 481
32AF5SOFTWAREGLU A:482 , ASN A:486 , SER A:487 , THR A:488 , THR A:508 , GLY B:75binding site for Poly-Saccharide residues NAG A 628 through FUL A 630 bound to ASN A 486
33AF6SOFTWAREASN B:17 , HOH B:703binding site for Mono-Saccharide NAG B 612 bound to ASN B 17
34AF7SOFTWAREARG B:14 , ASN B:57 , HOH B:783binding site for Mono-Saccharide NAG B 613 bound to ASN B 57
35AF8SOFTWAREASN B:106 , ASN B:188binding site for Mono-Saccharide NAG B 614 bound to ASN B 106
36AF9SOFTWARETYR B:237 , ASN B:241 , ASN B:245 , PHE B:278 , VAL B:280 , PRO B:281 , TYR B:282 , GLN B:380binding site for Poly-Saccharide residues NAG B 615 through FUL B 617 bound to ASN B 241
37AG1SOFTWAREGLU B:255 , ASN B:256binding site for Poly-Saccharide residues NAG B 618 through FUL B 620 bound to ASN B 256
38AG2SOFTWARESER B:338 , ASN B:341 , HOH B:735binding site for Mono-Saccharide NAG B 621 bound to ASN B 341
39AG3SOFTWAREARG A:240 , ASN A:241 , LEU A:244 , NAG A:622 , LYS B:427 , ASP B:454 , ASN B:455binding site for Poly-Saccharide residues NAG B 622 through FUL B 624 bound to ASN B 455
40AG4SOFTWAREILE B:305 , TYR B:477 , ASN B:481 , GLU B:482binding site for Mono-Saccharide NAG B 625 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  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:101 -Pro A:102
2Gln A:380 -Arg A:381
3Ala B:101 -Pro B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DYW)

(-) 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.............ee..................hhhhhh............eeeeeee......eeeeeee...........hhhhhhhhhhhhhh.eeeee...hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhh.......eeeeee...hhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....................eeeee......eee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dyw 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:525
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               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....hhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhh......................hhhhhhhh.......eeeeee...hhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...................eeeee......eee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dyw B   4 IIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV 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|      494       504       514       524     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         483|                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          485
   Legend:   → Mismatch (orange background)
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    → 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 5DYW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:101 - Pro A:102   [ RasMol ]  
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  5dyw
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  CHLE_HUMAN | P06276
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  3.1.1.8
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 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 5dyy 5k5e 5lkr

(-) Related Entries Specified in the PDB File

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