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(-) Description

Title :  CRYSTAL STRUCTURE OF PDE10A WITH A BIARYL ETHER INHIBITOR ((1-(3-(4-((1H-BENZO[D]IMIDAZOL-2-YL)AMINO)PHENOXY)PYRIDIN-2-YL)PIPERIDIN-4-YL)METHANOL)
 
Authors :  S. Chmait, S. Jordan
Date :  04 Oct 12  (Deposition) - 12 Dec 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Pde10A, Inhibitors, Phosphodiesterase 10A, Biaryl Ethers, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Rzasa, E. Hu, S. Rumfelt, N. Chen, K. L. Andrews, S. Chmait, J. R. Falsey, W. Zhong, A. D. Jones, A. Porter, S. W. Louie, X. Zhao, J. J. Treanor, J. R. Allen
Discovery Of Selective Biaryl Ethers As Pde10A Inhibitors: Improvement In Potency And Mitigation Of Pgp-Mediated Efflux.
Bioorg. Med. Chem. Lett. V. 22 7371 2012
PubMed-ID: 23149228  |  Reference-DOI: 10.1016/J.BMCL.2012.10.078

(-) Compounds

Molecule 1 - CAMP AND CAMP-INHIBITED CGMP 3',5'-CYCLIC PHOSPHODIESTERASE 10A
    Chains: A, B
    EC Number: 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 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
115J2Ligand/Ion(1-{3-[4-(1H-BENZIMIDAZOL-2-YLAMINO)PHENOXY]PYRIDIN-2-YL}PIPERIDIN-4-YL)METHANOL
2SO412Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 21)
No.NameCountTypeFull Name
115J3Ligand/Ion(1-{3-[4-(1H-BENZIMIDAZOL-2-YLAMINO)PHENOXY]PYRIDIN-2-YL}PIPERIDIN-4-YL)METHANOL
2SO418Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 21)
No.NameCountTypeFull Name
115J3Ligand/Ion(1-{3-[4-(1H-BENZIMIDAZOL-2-YLAMINO)PHENOXY]PYRIDIN-2-YL}PIPERIDIN-4-YL)METHANOL
2SO418Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:519 , HIS A:553 , ASP A:554 , ASP A:664 , ZN A:1002 , HOH A:1159 , HOH A:1275BINDING SITE FOR RESIDUE ZN A 1001
02AC2SOFTWAREASP A:554 , ZN A:1001 , HOH A:1152 , HOH A:1153 , HOH A:1155 , HOH A:1156 , HOH A:1275BINDING SITE FOR RESIDUE ZN A 1002
03AC3SOFTWAREPHE A:472 , GLU A:473 , ASN A:474 , ARG A:510 , ARG A:558 , HOH A:1276BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWARELYS A:497 , LEU A:595 , GLY A:597 , HIS A:598 , ASN A:599 , HOH A:1111BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWAREVAL A:512 , PRO A:513 , ARG A:558 , GLY A:559 , GLU A:685BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWARELEU A:537 , LEU A:646 , ASN A:647 , ARG A:652 , LEU B:646 , ARG B:652BINDING SITE FOR RESIDUE SO4 A 1006
07AC7SOFTWARELEU A:625 , PHE A:719 , 15J A:1009 , HOH A:1233BINDING SITE FOR RESIDUE SO4 A 1007
08AC8SOFTWARETRP A:672 , PRO A:673 , LYS A:676 , LYS A:694 , HOH A:1227BINDING SITE FOR RESIDUE SO4 A 1008
09AC9SOFTWARETYR A:514 , LEU A:665 , THR A:675 , ALA A:679 , 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 , SO4 A:1007 , HOH A:1126 , HOH A:1136 , HOH A:1190 , HOH A:1233BINDING SITE FOR RESIDUE 15J A 1009
10BC1SOFTWAREHIS B:519 , HIS B:553 , ASP B:554 , ASP B:664 , ZN B:802 , HOH B:901 , HOH B:956BINDING SITE FOR RESIDUE ZN B 801
11BC2SOFTWAREASP B:554 , ZN B:801 , HOH B:901 , HOH B:943 , HOH B:955 , HOH B:958 , HOH B:959BINDING SITE FOR RESIDUE ZN B 802
12BC3SOFTWAREPHE B:472 , GLU B:473 , ASN B:474 , ARG B:510 , ARG B:558 , HIS B:570 , HOH B:909 , HOH B:946BINDING SITE FOR RESIDUE SO4 B 803
13BC4SOFTWAREARG B:510 , ARG B:511 , HOH B:978 , HOH B:992BINDING SITE FOR RESIDUE SO4 B 804
14BC5SOFTWAREPRO B:673 , LYS B:694 , GLY B:697 , ILE B:698 , GLN B:699BINDING SITE FOR RESIDUE SO4 B 805
15BC6SOFTWAREPRO B:673 , LYS B:676 , LYS B:694BINDING SITE FOR RESIDUE SO4 B 806
16BC7SOFTWARELYS B:497 , GLY B:597 , HIS B:598 , ASN B:599 , HOH B:1036 , HOH B:1085BINDING SITE FOR RESIDUE SO4 B 807
17BC8SOFTWAREASN A:645 , THR B:539 , ASP B:540 , HOH B:1030BINDING SITE FOR RESIDUE SO4 B 808
18BC9SOFTWARETYR B:514 , LEU B:665 , THR B:675 , ALA B:679 , ILE B:682 , TYR B:683 , PHE B:686 , PRO B:702 , MET B:703 , LYS B:708 , GLU B:711 , GLY B:715 , GLN B:716 , PHE B:719 , HOH B:910 , HOH B:961BINDING SITE FOR RESIDUE 15J B 809

(-) 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 4HEU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HEU)

(-) 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 d4heua_ A: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh....hhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4heu 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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4heub_ B: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4heu B 452 FTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGE 759
                                   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
   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 4HEU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)

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        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 4hf4 4lkq 4llj 4llk 4llp 4llx 4lm0 4lm1 4lm2 4lm3 4lm4 4mrw 4mrz 4ms0 4msa 4msc 4mse 4msh 4msn 4muw 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

4ddl 4hf4