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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 2-1H-PYRAZOL-4-YLOXY-3H,4H-PYRIDO-3,4-D-PYRIMIDIN-4-ONE
 
Authors :  C. Chung
Date :  27 Nov 15  (Deposition) - 27 Jan 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Keywords :  Oxidoreductase, Inhibitor, Lysine Specific Histone Demethylase, Jmjd2D, Kdm4D, Jumonji (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Westaway, A. G. S. Preston, M. D. Barker, F. Brown, J. A. Brown, M. Campbell, C. Chung, H. Diallo, C. Douault, G. Drewes, R. Eagle, L. Gordon, C. Haslam, T. G. Hayhow, P. G. Humphreys, G. Joberty, R. Katso, L. Kruidenier, M. Leveridge, J. Liddle, J. Mosley, M. Muelbaier, R. Randle, I. Rioja, A. Rueger, G. A. Seal, R. J. Sheppard O. Singh, J. Taylor, P. Thomas, D. Thomson, D. M. Wilson, K. Lee, R. K. Prinjha
Cell Penetrant Inhibitors Of The Kdm4 And Kdm5 Families Of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives.
J. Med. Chem. V. 59 1357 2016
PubMed-ID: 26771107  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01537

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4D
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 11-341
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, JU MONJI DOMAIN-CONTAINING PROTEIN 2D, HUMAN LYSINE-SPECIFIC DEMETHYL ASE 4D, JMJD2D

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2HA61Ligand/Ion2-(1H-PYRAZOL-4-YLOXY)-3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
3SO47Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2HA61Ligand/Ion2-(1H-PYRAZOL-4-YLOXY)-3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
3SO47Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:238 , HIS A:244 , CYS A:310 , CYS A:312BINDING SITE FOR RESIDUE ZN A 350
02AC2SOFTWAREHIS A:192 , GLU A:194 , HIS A:280 , HA6 A:1341 , HOH A:2330 , HOH A:2335BINDING SITE FOR RESIDUE CO A 360
03AC3SOFTWAREHIS A:90 , TYR A:136 , ALA A:138 , TYR A:181 , THR A:188 , PHE A:189 , HIS A:192 , LYS A:210 , TRP A:212 , LYS A:245 , HIS A:280 , CO A:360 , HOH A:2194 , HOH A:2199 , HOH A:2330 , HOH A:2335BINDING SITE FOR RESIDUE HA6 A1341
04AC4SOFTWARETYR A:179 , TYR A:181 , GLU A:194 , ALA A:292 , ASN A:294 , HOH A:2431 , HOH A:2468 , HOH A:2469BINDING SITE FOR RESIDUE SO4 A1342
05AC5SOFTWAREARG A:60 , GLU A:61 , THR A:62 , ASN A:65 , HOH A:2151 , HOH A:2153 , HOH A:2161 , HOH A:2312BINDING SITE FOR RESIDUE SO4 A1343
06AC6SOFTWAREARG A:123 , LYS A:124 , LYS A:127 , ASN A:128 , HOH A:2261BINDING SITE FOR RESIDUE SO4 A1344
07AC7SOFTWAREPRO A:113 , LYS A:124 , ASN A:128 , TRP A:185 , LYS A:186 , HOH A:2261 , HOH A:2268BINDING SITE FOR RESIDUE SO4 A1345
08AC8SOFTWAREARG A:102 , HIS A:103 , ASN A:106 , HOH A:2215 , HOH A:2471BINDING SITE FOR RESIDUE SO4 A1346
09AC9SOFTWAREGLN A:116 , ASN A:117BINDING SITE FOR RESIDUE SO4 A1347
10BC1SOFTWAREASP A:302 , TYR A:303 , MET A:306BINDING SITE FOR RESIDUE SO4 A1348

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5FPB)

(-) Sequences/Alignments

Asymmetric Unit
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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:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee....hhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee...hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fpb A  11 AQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQ 340
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
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 Classification and Annotation

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (18, 18)

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  5fpb
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  KDM4D_HUMAN | Q6B0I6
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  1.14.11.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM4D_HUMAN | Q6B0I6: 3dxt 3dxu 4d6q 4d6r 4d6s 4hon 4hoo 5f5a 5f5c 5fp4 5fp7 5fp8 5fp9 5fpa 5ph0 5ph1 5ph2 5ph3 5ph4 5ph5 5ph6 5ph7 5ph8 5ph9 5pha 5phb 5phc 5phd 5phe 5phf 5phg 5phh 5phi 5phj 5phk 5phl 5phm 5phn 5pho 5php 5phq 5phr 5phs 5pht 5phu 5phv 5phw 5phx 5phy 5phz 5pi0 5pi1 5pi2 5pi3 5pi4 5pi5 5pi6 5pi7 5pi8 5pi9 5pia 5pib 5pic 5pid 5pie 5pif 5pig 5pih 5pii 5pij 5pik 5pil 5pim 5pin 5pio 5pip 5piq 5pir 5pis 5pit 5piu 5piv 5piw 5pix 5piy 5piz 5pj0 5pj1 5pj2 5pj3 5pj4 5pj5 5pj6 5pj7 5pj8 5pj9 5pja 5pjb 5pjc 5pjd 5pje 5pjf 5pjg 5pjh 5pji 5pjj 5pjk 5pjl 5pjm 5pjn 5pjo 5pjp 5pjq 5pjr 5pjs 5pjt 5pju 5pjv 5pjw 5pjx 5pjy 5pjz 5pk0 5pk1 5pk2 5pk3 5pk4 5pk5 5pk6 5pk7 5pk8 5pk9 5pka 5pkb 5pkc 5pkd 5pke 5pkf 5pkg 5pkh 5pki 5pkj 5pkk 5pkl 5pkm 5pkn 5pko 5pkp 5pkq 5pkr 5pks 5pkt 5pku 5pkv 5pkw 5pkx 5pky 5pkz 5pl0 5pl1 5pl2 5pl3 5pl4 5pl5 5pl6 5pl7 5pl8 5pl9 5pla 5plb 5plc 5pld 5ple 5plf 5plg 5plh 5pli 5plj 5plk 5pll 5plm 5pln 5plo 5plp 5plq 5plr 5pls 5plt 5plu 5plv 5plw 5plx 5ply 5plz 5pm0 5pm1 5pm2 5pm3 5pm4 5pm5 5pm6 5pm7 5pm8 5pm9 5pma 5pmb 5pmc 5pmd 5pme 5pmf 5pmg 5pmh 5pmi 5pmj 5pmk 5pml 5pmm 5pmn 5pmo 5pmp 5pmq 5pmr 5pms 5pmt 5pmu 5pmv 5pmw 5pmx 5pmy 5pmz 5pn0 5pn1 5pn2 5pn3 5pn4 5pn5 5pn6 5pn7 5pn8 5pn9 5pna 5pnb 5pnc 5pnd 5pne 5pnf 5png 5pnh 5pni 5pnj 5pnk 5pnl 5pnm 5pnn 5pno 5pnp 5pnq 5pnr 5pns 5pnu 5pnv 5pnw

(-) Related Entries Specified in the PDB File

5fp3 CELL PENETRANT INHIBITORS OF THE JMJD2 (KDM4) AND JARID1 (KDM5) FAMILIES OF HISTONE LYSINE DEMETHYLASES
5fp4 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-( 4-PHENYLBUTANAMIDO)PYRIDINE-4-CARBOXYLIC ACID
5fp7 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-4 -METHYLTHIOPHEN-2-YL METHYLAMINOPYRIDINE-4-CARBOXYLIC ACID
5fp8 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-4 -METHYLTHIOPHEN-2-YLMETHYLAMINOPYRIDINE-4-CARBOXYLIC ACID
5fp9 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3- AMINOPYRIDINE-4-CARBOXYLIC ACID
5fpa CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3H, 4H-PYRIDO-3,4-D-PYRIMIDIN-4-ONE