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(-) Description

Title :  CRYSTAL STRUCTURE OF PDE10A WITH NOVEL KETO-BENZIMIDAZOLE INHIBITOR
 
Authors :  S. Chmait, S. Jordan
Date :  24 Sep 13  (Deposition) - 23 Oct 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
12F52Ligand/Ion1H-BENZIMIDAZOL-2-YL(4-{[3-(MORPHOLIN-4-YL)PYRAZIN-2-YL]OXY}PHENYL)METHANONE
2SO412Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
12F52Ligand/Ion1H-BENZIMIDAZOL-2-YL(4-{[3-(MORPHOLIN-4-YL)PYRAZIN-2-YL]OXY}PHENYL)METHANONE
2SO412Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 24)
No.NameCountTypeFull Name
12F53Ligand/Ion1H-BENZIMIDAZOL-2-YL(4-{[3-(MORPHOLIN-4-YL)PYRAZIN-2-YL]OXY}PHENYL)METHANONE
2SO421Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 18)
No.NameCountTypeFull Name
12F53Ligand/Ion1H-BENZIMIDAZOL-2-YL(4-{[3-(MORPHOLIN-4-YL)PYRAZIN-2-YL]OXY}PHENYL)METHANONE
2SO415Ligand/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:1002BINDING SITE FOR RESIDUE ZN A 1001
02AC2SOFTWAREASP A:554 , ZN A:1001BINDING SITE FOR RESIDUE ZN A 1002
03AC3SOFTWAREPHE A:472 , GLU A:473 , ASN A:474 , MET A:475 , ARG A:510 , ARG A:558 , HIS A:570BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWARELYS A:497 , GLY A:597 , HIS A:598 , ASN A:599 , HOH A:1159BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWAREASN A:647 , ARG A:652 , LEU B:537 , LEU B:646 , ASN B:647 , ARG B:652BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWAREARG A:510 , ARG A:511BINDING SITE FOR RESIDUE SO4 A 1006
07AC7SOFTWARESER A:577 , THR A:578 , GLN A:583BINDING SITE FOR RESIDUE SO4 A 1007
08AC8SOFTWAREASN A:508 , GLN A:588 , SER A:591BINDING SITE FOR RESIDUE SO4 A 1008
09AC9SOFTWAREASP A:468 , LYS A:518 , THR A:678 , LYS A:695 , HOH A:1144BINDING SITE FOR RESIDUE SO4 A 1009
10BC1SOFTWARETYR A:514 , SER A:667 , VAL A:668 , ILE A:682 , TYR A:683 , PHE A:686 , PRO A:702 , MET A:703 , LYS A:708 , GLY A:715 , GLN A:716 , PHE A:719 , HOH A:1140BINDING SITE FOR RESIDUE 2F5 A 1010
11BC2SOFTWAREHIS B:519 , HIS B:553 , ASP B:554 , ASP B:664 , ZN B:802 , HOH B:901BINDING SITE FOR RESIDUE ZN B 801
12BC3SOFTWAREASP B:554 , ZN B:801 , HOH B:927BINDING SITE FOR RESIDUE ZN B 802
13BC4SOFTWAREPHE B:472 , GLU B:473 , ASN B:474 , MET B:475 , ARG B:510 , ARG B:558 , HIS B:570BINDING SITE FOR RESIDUE SO4 B 803
14BC5SOFTWAREARG B:510 , ARG B:511BINDING SITE FOR RESIDUE SO4 B 804
15BC6SOFTWARELYS B:497 , GLY B:597 , HIS B:598 , ASN B:599BINDING SITE FOR RESIDUE SO4 B 805
16BC7SOFTWAREASN A:645 , ASN A:647 , ASN A:648 , THR B:539 , ASP B:540BINDING SITE FOR RESIDUE SO4 B 806
17BC8SOFTWAREASN B:508 , GLN B:588 , SER B:591 , ILE B:592BINDING SITE FOR RESIDUE SO4 B 807
18BC9SOFTWARESER B:667 , VAL B:668 , ILE B:682 , TYR B:683 , PHE B:686 , PRO B:702 , MET B:703 , GLU B:711 , VAL B:712 , GLY B:715 , GLN B:716 , PHE B:719BINDING SITE FOR RESIDUE 2F5 B 808

(-) 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 4MVH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MVH)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4mvha_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvh A 453 TLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGE 759
                                   462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4mvhb_ B: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mvh 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 4MVH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)

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(-) 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 4muw 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

4muw