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(-) Description

Title :  HUMAN BUTYRYLCHOLINESTERASE IN COMPLEX WITH N-((1-(2,3-DIHYDRO-1H-INDEN-2-YL)PIPERIDIN-3-YL)METHYL)-N-(2-METHOXYETHYL)-2-NAPHTHAMIDE
 
Authors :  N. Coquelle, B. Brus, J. P. Colletier, S. Gobec
Date :  07 Jun 14  (Deposition) - 22 Oct 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Butyrylcholinesterase Inhibition, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Brus, U. Kosak, S. Turk, A. Pislar, N. Coquelle, J. Kos, J. Stojan, J. P. Colletier, S. Gobec
Discovery, Biological Evaluation, And Crystal Structure Of Novel Nanomolar Selective Butyrylcholinesterase Inhibitor.
J. Med. Chem. V. 57 8167 2014
PubMed-ID: 25226236  |  Reference-DOI: 10.1021/JM501195E

(-) Compounds

Molecule 1 - CHOLINESTERASE
    Chains: A, B
    EC Number: 3.1.1.8
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    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 Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 34)

Asymmetric Unit (6, 34)
No.NameCountTypeFull Name
13F92Ligand/IonN-{[(3R)-1-(2,3-DIHYDRO-1H-INDEN-2-YL)PIPERIDIN-3-YL]METHYL}-N-(2-METHOXYETHYL)NAPHTHALENE-2-CARBOXAMIDE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3FUC2Ligand/IonALPHA-L-FUCOSE
4FUL2Ligand/IonBETA-L-FUCOSE
5GOL5Ligand/IonGLYCEROL
6NAG20Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (6, 18)
No.NameCountTypeFull Name
13F91Ligand/IonN-{[(3R)-1-(2,3-DIHYDRO-1H-INDEN-2-YL)PIPERIDIN-3-YL]METHYL}-N-(2-METHOXYETHYL)NAPHTHALENE-2-CARBOXAMIDE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3FUC2Ligand/IonALPHA-L-FUCOSE
4FUL1Ligand/IonBETA-L-FUCOSE
5GOL1Ligand/IonGLYCEROL
6NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (5, 16)
No.NameCountTypeFull Name
13F91Ligand/IonN-{[(3R)-1-(2,3-DIHYDRO-1H-INDEN-2-YL)PIPERIDIN-3-YL]METHYL}-N-(2-METHOXYETHYL)NAPHTHALENE-2-CARBOXAMIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FUC-1Ligand/IonALPHA-L-FUCOSE
4FUL1Ligand/IonBETA-L-FUCOSE
5GOL4Ligand/IonGLYCEROL
6NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:68 , ILE A:69 , ASP A:70 , TRP A:82 , GLY A:116 , GLY A:117 , GLU A:197 , SER A:198 , PHE A:329 , TYR A:332 , GLY A:439 , HOH A:767 , HOH A:781binding site for residue 3F9 A 615
02AC2SOFTWAREASN A:228 , CYS A:400 , PRO A:401binding site for residue GOL A 616
03AC3SOFTWAREHIS A:77 , GLU A:443binding site for residue EDO A 617
04AC4SOFTWARELEU A:18 , TRP A:98 , ASP A:129 , LYS A:131binding site for residue EDO A 618
05AC5SOFTWARENAG B:605binding site for residue NDG B 607
06AC6SOFTWAREASP B:70 , TRP B:82 , GLY B:116 , SER B:198 , TRP B:231 , LEU B:286 , PHE B:329 , TYR B:332 , HOH B:753 , HOH B:785binding site for residue 3F9 B 611
07AC7SOFTWARELEU B:18 , TYR B:61 , TRP B:98 , ASP B:129 , LYS B:131binding site for residue GOL B 612
08AC8SOFTWAREHIS B:372 , TYR B:373 , THR B:374 , ASP B:375 , GLN B:518 , HOH B:783binding site for residue GOL B 613
09AC9SOFTWARESER A:489 , ILE B:69 , GLN B:71 , SER B:72 , HOH B:740binding site for residue GOL B 614
10AD1SOFTWAREHIS B:77 , MET B:81 , GLU B:443binding site for residue GOL B 615
11AD2SOFTWAREARG B:42 , LYS B:267binding site for residue EDO B 616
12AD3SOFTWAREASN A:17binding site for Mono-Saccharide NAG A 601 bound to ASN A 17
13AD4SOFTWAREASP A:54 , ILE A:55 , ASN A:57binding site for Poly-Saccharide residues NAG A 602 through FUL A 603 bound to ASN A 57
14AD5SOFTWARELYS A:105 , ASN A:106 , ASN A:188 , LYS A:190binding site for Poly-Saccharide residues NAG A 604 through NAG A 605 bound to ASN A 106
15AD6SOFTWAREASN A:241 , ASN A:245 , PHE A:278binding site for Poly-Saccharide residues NAG A 606 through FUC A 607 bound to ASN A 241
16AD7SOFTWAREPRO A:335 , GLY A:336 , SER A:338 , ASN A:341binding site for Poly-Saccharide residues NDG A 608 through FUC A 610 bound to ASN A 341
17AD8SOFTWARETYR A:477 , ASN A:481 , GLU A:482 , GLN A:484 , LEU B:88 , GLN B:270binding site for Poly-Saccharide residues NAG A 611 through NAG A 612 bound to ASN A 481
18AD9SOFTWAREASN A:486binding site for Poly-Saccharide residues NAG A 613 through NAG A 614 bound to ASN A 486
19AE1SOFTWAREASN B:17 , THR B:24binding site for Mono-Saccharide NAG B 601 bound to ASN B 17
20AE2SOFTWAREARG B:14 , ASP B:54 , ILE B:55 , ASN B:57binding site for Mono-Saccharide NAG B 602 bound to ASN B 57
21AE3SOFTWAREASN B:106 , ASN B:188 , LYS B:190 , HOH B:718binding site for Poly-Saccharide residues NAG B 603 through NAG B 604 bound to ASN B 106
22AE4SOFTWAREASN B:241 , ASN B:245 , LYS B:248 , PHE B:278 , HOH B:748binding site for Poly-Saccharide residues NAG B 605 through FUL B 606 bound to ASN B 241
23AE5SOFTWAREASN B:256 , HOH B:745binding site for Mono-Saccharide NAG B 608 bound to ASN B 256
24AE6SOFTWAREASN B:341 , ASN B:342 , HOH B:746 , HOH B:747 , HOH B:789binding site for Mono-Saccharide NAG B 609 bound to ASN B 341
25AE7SOFTWAREASN B:481 , GLU B:482 , HOH B:780binding site for Mono-Saccharide NDG B 610 bound to ASN B 481

(-) SS Bonds  (6, 6)

Asymmetric 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 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 4TPK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TPK)

(-) Exons   (0, 0)

(no "Exon" information available for 4TPK)

(-) 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:528
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeee.eeeee..eeeeeeeeee.....hhhhh............eee..................hhhhhh............eeeeeeee.....eeeeeee...........hhhhhhhhhhhhhh.eeeee....hhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhh.....................hhhhhhhh.......eeeeee...hhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....................eeeee......eee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tpk A   3 DIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKVL 530
                                    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............eeeeeeee.....eeeeeee...........hhhhhhhhhhhhhh.eeeee....hhhhhh..........hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhh.....................hhhhhhhhh......eeeeee...hhhhhh..............hhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..................eeeee......eee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tpk B   4 IIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKVL 530
                                    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|      495       505       515       525     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         483|                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          486
   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 4TPK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TPK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TPK)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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  CHLE_HUMAN | P06276
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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 4xii 5dyt 5dyw 5dyy 5k5e 5lkr

(-) Related Entries Specified in the PDB File

4bds 4BDS IS THE SAME PROTEIN COMPLEXED WITH TACRINE