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(-) Description

Title :  CRYSTAL STRUCTURE OF PDE10A WITH NOVEL KETO-BENZIMIDAZOLE INHIBITOR
 
Authors :  S. Chmait, S. Jordan
Date :  23 Sep 13  (Deposition) - 23 Oct 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (3x)
Biol. Unit 3:  B  (3x)
Keywords :  Pde10A, Phosphodiesterase 10A, Inhibitors, Keto-Benzimidazoles, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Hu, R. K. Kunz, N. Chen, S. Rumfelt, A. Siegmund, K. Andrews, S. Chmait, S. Zhao, C. Davis, H. Chen, D. Lester-Zeiner, J. Ma, C. Biorn J. Shi, A. Porter, J. Treanor, J. R. Allen
Design, Optimization, And Biological Evaluation Of Novel Keto-Benzimidazoles As Potent And Selective Inhibitors Of Phosphodiesterase 10A (Pde10A).
J. Med. Chem. V. 56 8781 2013
PubMed-ID: 24102193  |  Reference-DOI: 10.1021/JM401234W

(-) Compounds

Molecule 1 - CAMP AND CAMP-INHIBITED CGMP 3',5'-CYCLIC PHOSPHODIESTERASE 10A
    Chains: A, B
    EC Number: 3.1.4.17, 3.1.4.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: HUMAN PDE10A, RESIDUES 442-779
    Gene: PDE10A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): A 
Biological Unit 3 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
12F42Ligand/Ion2-{4-[(6,7-DIFLUORO-1H-BENZIMIDAZOL-2-YL)AMINO]PHENOXY}-N-METHYL-3,4'-BIPYRIDIN-2'-AMINE
2GOL1Ligand/IonGLYCEROL
3SO415Ligand/IonSULFATE ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
12F42Ligand/Ion2-{4-[(6,7-DIFLUORO-1H-BENZIMIDAZOL-2-YL)AMINO]PHENOXY}-N-METHYL-3,4'-BIPYRIDIN-2'-AMINE
2GOL1Ligand/IonGLYCEROL
3SO415Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 30)
No.NameCountTypeFull Name
12F43Ligand/Ion2-{4-[(6,7-DIFLUORO-1H-BENZIMIDAZOL-2-YL)AMINO]PHENOXY}-N-METHYL-3,4'-BIPYRIDIN-2'-AMINE
2GOL3Ligand/IonGLYCEROL
3SO424Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 24)
No.NameCountTypeFull Name
12F43Ligand/Ion2-{4-[(6,7-DIFLUORO-1H-BENZIMIDAZOL-2-YL)AMINO]PHENOXY}-N-METHYL-3,4'-BIPYRIDIN-2'-AMINE
2GOL-1Ligand/IonGLYCEROL
3SO421Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:519 , HIS A:553 , ASP A:554 , ASP A:664 , ZN A:1002BINDING SITE FOR RESIDUE ZN A 1001
02AC2SOFTWAREASP A:554 , ZN A:1001 , HOH A:1104 , HOH A:1170 , HOH A:1171 , HOH A:1172BINDING SITE FOR RESIDUE ZN A 1002
03AC3SOFTWAREPHE A:472 , GLU A:473 , ASN A:474 , ARG A:510 , ARG A:558BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWARELYS A:497 , LEU A:595 , GLY A:597 , HIS A:598 , ASN A:599 , HOH A:1129BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWAREVAL A:512 , PRO A:513 , ARG A:558 , GLY A:559 , GLU A:685 , ALA A:688BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWARELEU A:537 , LEU A:646 , ASN A:647 , ARG A:652 , LEU B:537 , LEU B:646 , ASN B:647 , ARG B:652BINDING SITE FOR RESIDUE SO4 A 1006
07AC7SOFTWAREARG A:510 , ARG A:511BINDING SITE FOR RESIDUE SO4 A 1007
08AC8SOFTWARESER A:577 , THR A:578 , GLN A:583BINDING SITE FOR RESIDUE SO4 A 1008
09AC9SOFTWAREASN A:508 , GLN A:588 , SER A:591BINDING SITE FOR RESIDUE SO4 A 1009
10BC1SOFTWAREARG A:486 , GLN A:532 , HIS A:535 , HOH A:1102 , HOH A:1144 , THR B:641 , GLY B:642BINDING SITE FOR RESIDUE SO4 A 1010
11BC2SOFTWAREGLN A:634 , SER A:650 , ARG A:654BINDING SITE FOR RESIDUE GOL A 1011
12BC3SOFTWARETYR A:514 , LEU A:625 , ILE A:682 , TYR A:683 , PHE A:686 , PRO A:702 , MET A:703 , LYS A:708 , GLU A:711 , GLY A:715 , GLN A:716 , PHE A:719 , HOH A:1185BINDING SITE FOR RESIDUE 2F4 A 1012
13BC4SOFTWAREHIS B:519 , HIS B:553 , ASP B:554 , ASP B:664 , ZN B:802 , HOH B:970BINDING SITE FOR RESIDUE ZN B 801
14BC5SOFTWAREASP B:554 , ZN B:801 , HOH B:904 , HOH B:914 , HOH B:969BINDING SITE FOR RESIDUE ZN B 802
15BC6SOFTWAREPHE B:472 , GLU B:473 , ASN B:474 , ARG B:510 , ARG B:558 , HOH B:918BINDING SITE FOR RESIDUE SO4 B 803
16BC7SOFTWAREARG B:510 , ARG B:511 , HOH B:916BINDING SITE FOR RESIDUE SO4 B 804
17BC8SOFTWAREPRO B:673 , LYS B:694 , GLY B:697 , ILE B:698 , GLN B:699BINDING SITE FOR RESIDUE SO4 B 805
18BC9SOFTWARELYS B:497 , GLY B:597 , HIS B:598 , ASN B:599BINDING SITE FOR RESIDUE SO4 B 806
19CC1SOFTWAREASN A:645 , THR B:539 , ASP B:540 , HOH B:923 , HOH B:925BINDING SITE FOR RESIDUE SO4 B 807
20CC2SOFTWAREASN B:508 , GLN B:588 , SER B:591 , ILE B:592BINDING SITE FOR RESIDUE SO4 B 808
21CC3SOFTWAREVAL B:512 , PRO B:513 , ARG B:558 , GLY B:559 , PHE B:560 , GLU B:685 , ALA B:688BINDING SITE FOR RESIDUE SO4 B 809
22CC4SOFTWARELEU B:625 , VAL B:668 , ILE B:682 , TYR B:683 , PHE B:686 , PRO B:702 , LYS B:708 , GLU B:711 , VAL B:712 , GLY B:715 , GLN B:716 , PHE B:719BINDING SITE FOR RESIDUE 2F4 B 810

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:488 -A:492
2B:488 -B:492

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MUW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MUW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MUW)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4muwa_ A: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh....hhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4muw A 442 TSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGE 759
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751        


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4muwb_ B: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4muw B 454 LPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGE 759
                                   463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753
   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  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)

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  4muw
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE10_HUMAN | Q9Y233: 1lrb 2oun 2oup 2ouq 2our 2ous 2ouu 2ouv 2ouy 2wey 2y0j 2zmf 3sn7 3sni 3snl 3ui7 3uuo 3wi2 3ws8 3ws9 3wyk 3wyl 3wym 4ael 4ajd 4ajf 4ajg 4ajm 4bbx 4ddl 4dff 4fcb 4fcd 4heu 4hf4 4lkq 4llj 4llk 4llp 4llx 4lm0 4lm1 4lm2 4lm3 4lm4 4mrw 4mrz 4ms0 4msa 4msc 4mse 4msh 4msn 4mvh 4p0n 4p1r 4phw 4tpm 4tpp 4wn1 4xy2 4yqh 4ys7 4zo5 5axp 5axq 5b4k 5b4l 5c1w 5c28 5c29 5c2a 5c2e 5c2h 5dh4 5dh5 5ede 5edg 5edh 5edi 5i2r 5k9r 5uwf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4MUW)