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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT 2-PIPERIDIN-4-YLOXY-5-(TRIFLUOROMETHYL)PYRIDINE (N10072A) (LIGAND MODELLED BASED ON PANDDA EVENT MAP)
 
Authors :  R. Nowak, T. Krojer, N. Pearce, C. Johansson, C. Gileadi, K. Kupinska, C. Strain-Damerell, A. Szykowska, N. A. Burgess-Brown, C. H. Arrowsm C. Bountra, A. M. Edwards, F. Von Delft, P. E. Brennan, U. Oppermann
Date :  12 Mar 16  (Deposition) - 30 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Jarid1B, Plu1, Pandda, Fragment Screening, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Nowak, T. Krojer, N. Pearce, C. Johansson, C. Gileadi, K. Kupinska, C. Strain-Damerell, A. Szykowska, N. A. Burgess-Brown, C. H. Arrowsmith, C. Bountra, A. M. Edwards, F. Von Delft, P. E. Brennan, U. Oppermann
Crystal Structure Of The Catalytic Domain Of Human Jarid1B In Complex With 3D Fragment 2-Piperidin-4-Yloxy-5- (Trifluoromethyl)Pyridine (N10072A) (Ligand Modelled Based On Pandda Event Map)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 5B
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFB-LIC-BSE
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: JMJC DOMAIN, UNP RESIDUES 26-101,374-770
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B, JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA-BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 19)

Asymmetric/Biological Unit (6, 19)
No.NameCountTypeFull Name
180Q1Ligand/Ion2-PIPERIDIN-4-YLOXY-5-(TRIFLUOROMETHYL)PYRIDINE
2CL1Ligand/IonCHLORIDE ION
3DMS4Ligand/IonDIMETHYL SULFOXIDE
4EDO10Ligand/Ion1,2-ETHANEDIOL
5MN1Ligand/IonMANGANESE (II) ION
6ZN2Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:692 , CYS A:695 , CYS A:715 , HIS A:718BINDING SITE FOR RESIDUE ZN A1754
02AC2SOFTWARECYS A:706 , CYS A:708 , CYS A:723 , CYS A:725BINDING SITE FOR RESIDUE ZN A1755
03AC3SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2061BINDING SITE FOR RESIDUE CL A1756
04AC4SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , HOH A:2130 , HOH A:2131 , HOH A:2138BINDING SITE FOR RESIDUE MN A1757
05AC5SOFTWAREGLU A:662 , LYS A:663 , ARG A:666 , GLU A:667 , MET A:701 , TYR A:736 , THR A:737 , LEU A:738 , LEU A:741 , HOH A:2276BINDING SITE FOR RESIDUE 80Q A1758
06AC6SOFTWAREPHE A:83 , GLY A:426 , ALA A:427 , ASP A:428 , PHE A:434 , LEU A:487 , TYR A:488 , VAL A:489 , HOH A:2108BINDING SITE FOR RESIDUE EDO A1759
07AC7SOFTWAREARG A:666 , SER A:677 , TYR A:734 , HOH A:2278 , HOH A:2279BINDING SITE FOR RESIDUE EDO A1760
08AC8SOFTWAREARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , LEU A:665BINDING SITE FOR RESIDUE EDO A1761
09AC9SOFTWAREPRO A:30 , VAL A:568 , TYR A:569 , HOH A:2280BINDING SITE FOR RESIDUE EDO A1762
10BC1SOFTWAREASP A:688 , GLU A:689 , ARG A:690 , GLN A:691 , GLY A:711 , LEU A:713BINDING SITE FOR RESIDUE EDO A1763
11BC2SOFTWAREGLY A:524 , TYR A:525 , HOH A:2282BINDING SITE FOR RESIDUE EDO A1764
12BC3SOFTWAREARG A:670 , VAL A:674 , ILE A:675 , HOH A:2104 , HOH A:2217BINDING SITE FOR RESIDUE EDO A1765
13BC4SOFTWARETRP A:504 , GLU A:531 , ARG A:584 , HIS A:617 , TYR A:618 , ARG A:623 , HOH A:2136 , HOH A:2193BINDING SITE FOR RESIDUE EDO A1766
14BC5SOFTWARETYR A:425 , SER A:494 , SER A:495 , ASN A:591 , DMS A:1769 , DMS A:1770 , HOH A:2105 , HOH A:2155BINDING SITE FOR RESIDUE EDO A1767
15BC6SOFTWAREHOH A:2250 , HOH A:2283BINDING SITE FOR RESIDUE EDO A1768
16BC7SOFTWARETYR A:488 , PHE A:496 , ASN A:509 , LYS A:517 , TRP A:519 , EDO A:1767 , HOH A:2155BINDING SITE FOR RESIDUE DMS A1769
17BC8SOFTWAREGLN A:88 , GLN A:96 , TYR A:425 , SER A:495 , PHE A:496 , CYS A:497 , EDO A:1767BINDING SITE FOR RESIDUE DMS A1770
18BC9SOFTWARECYS A:634 , LYS A:635 , GLU A:683 , PHE A:700 , ARG A:735 , TYR A:736BINDING SITE FOR RESIDUE DMS A1771
19CC1SOFTWARETRP A:486 , TYR A:488 , SER A:507 , ALA A:599 , VAL A:600 , ASN A:601 , HOH A:2124 , HOH A:2142BINDING SITE FOR RESIDUE DMS A1772

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FZA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FZA)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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(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:453
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee....eehhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh......eeeeeeee................hhhhhhh........hhhhh...........hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh...hhhh.ee...hhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhh...........eeeee........hhhhhhhh...hhh.eeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fza A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAE 753
                             ||     33        43        53        63        73        83        93      |378       388       398       408       418       428       438   ||  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   
                             0|                                                                       100|                                                               442|                                                                                                                                                                                                                                                                                                                    
                             26                                                                        376                                                                445
   Legend:   → Mismatch (orange background)
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    → 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 5FZA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

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UniProtKB/Swiss-Prot
        KDM5B_HUMAN | Q9UGL1: 2ma5 2mny 2mnz 5a1f 5a3n 5a3p 5a3t 5a3w 5fpl 5fpu 5fun 5fup 5fv3 5fy4 5fy5 5fy9 5fyb 5fys 5fyt 5fyu 5fyv 5fyy 5fyz 5fz0 5fz1 5fz3 5fz4 5fz6 5fz7 5fz8 5fz9 5fzb 5fzc 5fzd 5fze 5fzf 5fzg 5fzh 5fzi 5fzk 5fzl 5fzm 5lw9 5lwb

(-) Related Entries Specified in the PDB File

5fyb CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC1648
5fyc CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH SUCCINATE
5fyh CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH FUMARATE
5fyi CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH PYRUVATE
5fym CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH D-2-HYDROXYGLUTARATE
5fys CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH D-2-HYDROXYGLUTARATE
5fyt CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N09996A
5fyu CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10042A
5fyv CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH OXALOACETATE
5fyy CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N05798A
5fyz CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10063A
5fz0 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N11213A
5fz1 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH E48115B
5fz3 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N08776B
5fz4 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10057A
5fz6 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT N05859B ( LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fz7 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT ETHYL 2- AMINO-4-THIOPHEN-2-YLTHIOPHENE-3-CARBOXYLATE (N06131B ) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fz8 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MALATE
5fz9 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT THIENO(3,2 -B)THIOPHENE-5-CARBOXYLIC ACID (N06263B) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04 -1 FRAGMENT SCREENING)
5fzb CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT 4- PYRIDYLTHIOUREA (N06275B) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fzc CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT 4,5- DIHYDRONAPHTHO(1,2-B)THIOPHENE-2-CARBOXYLICACID (N11181A ) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fzd CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH L-2-HYDROXYGLUTARATE
5fze CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC3960
5fzf CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC3962
5fzg CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC3948
5fzh CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT 4,5- DIHYDRONAPHTHO(1,2-B)THIOPHENE-2-CARBOXYLICACID (N11181A ) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fzi CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC3095
5fzk CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT N,3-DIMETHYL-N -(PYRIDIN-3-YLMETHYL)-1,2-OXAZOLE-5-CARBOXAMIDE ( N10051A) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fzl CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT 3-METHYL-N- PYRIDIN-4-YL-1,2-OXAZOLE-5-CARBOXAMIDE (N09954A) ( LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fzm CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT 5-(2-FLUOROPHENYL )-1,3-OXAZOLE-4-CARBOXYLIC ACID (N09989B) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04 -1 FRAGMENT SCREENING)
5fzo CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JMJD1C