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(-) Description

Title :  THIENO[3,2-B]PYRROLE-5-CARBOXAMIDES AS NOVEL REVERSIBLE INHIBITORS OF HISTONE LYSINE DEMETHYLASE KDM1A/LSD1: COMPOUND 34
 
Authors :  A. Mattevi, G. Ciossani
Date :  08 Jul 16  (Deposition) - 22 Feb 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Vianello, L. Sartori, F. Amigoni, A. Cappa, G. Faga, R. Fattori, E. Legnaghi, G. Ciossani, A. Mattevi, G. Meroni, L. Moretti, V. Cecatiello, S. Pasqualato, A. Romussi, F. Thaler, P. Trifiro, M. Villa, O. A. Botrugno, P. Dessanti, S. Minucci, S. Vultaggio, E. Zagarri, M. Varasi, C. Mercurio
Thieno[3, 2-B]Pyrrole-5-Carboxamides As New Reversible Inhibitors Of Histone Lysine Demethylase Kdm1A/Lsd1. Part 2 Structure-Based Drug Design And Structure-Activity Relationship.
J. Med. Chem. V. 60 1693 2017
PubMed-ID: 28186757  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01019

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A
    Chains: A
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BRAF35-HDAC COMPLEX PROTEIN BHC110,FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2
 
Molecule 2 - REST COREPRESSOR 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RCOR1, KIAA0071, RCOR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN COREST

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
16W11Ligand/Ion4-METHYL-~{N}-[2-[[4-[[(3~{R})-PYRROLIDIN-3-YL]METHOXY]PHENOXY]METHYL]PHENYL]THIENO[3,2-B]PYRROLE-5-CARBOXAMIDE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:285 , GLY A:287 , VAL A:288 , SER A:289 , LEU A:307 , GLU A:308 , ALA A:309 , ARG A:310 , GLY A:314 , GLY A:315 , ARG A:316 , LEU A:329 , GLY A:330 , ALA A:331 , MET A:332 , VAL A:333 , THR A:588 , ALA A:589 , VAL A:590 , THR A:624 , LEU A:625 , PRO A:626 , TRP A:756 , SER A:760 , TYR A:761 , GLY A:800 , GLU A:801 , ALA A:809 , THR A:810 , VAL A:811 , ALA A:814 , 6W1 A:902binding site for residue FAD A 901
2AC2SOFTWARETHR A:335 , ALA A:539 , ASP A:555 , TRP A:695 , TYR A:761 , ALA A:809 , FAD A:901binding site for residue 6W1 A 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LGU)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:240 -Pro A:241
2Pro A:470 -Pro A:471
3Gln A:633 -Pro A:634
4Val A:640 -Pro A:641

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LGU)

(-) 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:666
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.......hhhhhhhhhhhhhhh....................eeeee..hhhhhhhhhhhhhh..eeeee...........eeee..eeee....eee....hhhhhhhhhh...eee...............hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh...........hhhhhhh....eeee....hhhhhhhh....ee..eeeeeeeee..eeeeeeee......eeeeee.eeee..hhhhhhh.....eee...hhhhhhhhhhhee...eeeeee...........eee..........eeeeeee.....eeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh........eeee.............ee.....hhhhhhhhhh.................eee...........hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lgu A 171 PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTL 836
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830      


Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh............hhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgu B 308 RKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE 440
                                   317       327       337       347       357       367       377       387       397       407       417       427       437
   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  (0, 0)

(no "SCOP Domain" information available for 5LGU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (71, 85)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:240 - Pro A:241   [ RasMol ]  
    Gln A:633 - Pro A:634   [ RasMol ]  
    Pro A:470 - Pro A:471   [ RasMol ]  
    Val A:640 - Pro A:641   [ RasMol ]  
 

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  5lgu
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  KDM1A_HUMAN | O60341
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM1A_HUMAN | O60341: 2com 2dw4 2ejr 2h94 2hko 2iw5 2l3d 2uxn 2uxx 2v1d 2x0l 2xaf 2xag 2xah 2xaj 2xaq 2xas 2y48 2z3y 2z5u 3abt 3abu 3zms 3zmt 3zmu 3zmv 3zmz 3zn0 3zn1 4bay 4czz 4kum 4uv8 4uv9 4uva 4uvb 4uvc 4uxn 4xbf 5afw 5h6q 5h6r 5it3 5l3b 5l3c 5l3d 5l3e 5l3f 5l3g 5lbq 5lgn 5lgt 5lhg 5lhh 5lhi 5x60
        RCOR1_HUMAN | Q9UKL0: 2iw5 2uxn 2uxx 2v1d 2x0l 2xaf 2xag 2xah 2xaj 2xaq 2xas 2y48 3zms 3zmt 3zmu 3zmv 3zmz 3zn0 3zn1 4bay 4kum 4uv8 4uv9 4uva 4uvb 4uvc 4uxn 4xbf 5h6q 5h6r 5l3b 5l3c 5l3d 5l3e 5l3f 5l3g 5lbq 5lgn 5lgt 5lhg 5lhh 5lhi 5x60

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LGU)