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5F2W
Biol. Unit 4
Info
Asym.Unit (483 KB)
Biol.Unit 1 (120 KB)
Biol.Unit 2 (123 KB)
Biol.Unit 3 (123 KB)
Biol.Unit 4 (123 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN KDM4A IN COMPLEX WITH COMPOUND 16
Authors
:
Y. -V. Le Bihan, S. Dempster, I. M. Westwood, R. L. M. Van Montfort
Date
:
02 Dec 15 (Deposition) - 20 Jan 16 (Release) - 09 Mar 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Epigenetics, Demethylase, Inhibitor, Oxidoreductase-Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Bavetsias, R. M. Lanigan, G. F. Ruda, B. Atrash, M. G. Mclaughlin, A. Tumber, N. Y. Mok, Y. V. Le Bihan, S. Dempster, K. J. Boxall, F. Jeganathan, S. B. Hatch, P. Savitsky, S. Velupillai, T. Krojer, K. S. England, J. Sejberg, C. Thai, A. Donovan, A. Pal, G. Scozzafava, J. M. Bennett, A. Kawamura, C. Johansson, A. Szykowska, C. Gileadi, N. A. Burgess-Brown, F. Von Delft, U. Oppermann, Z. Walters, J. Shipley, F. I. Raynaud, S. M. Westaway, R. K. Prinjha, O. Fedorov, R. Burke, C. J. Schofield, I. M. Westwood, C. Bountra, S. Muller, R. L. Van Montfort, P. E. Brennan, J. Blagg
8-Substituted Pyrido[3, 4-D]Pyrimidin-4(3H)-One Derivatives As Potent, Cell Permeable, Kdm4 (Jmjd2) And Kdm5 (Jarid1) Histone Lysine Demethylase Inhibitors.
J. Med. Chem. V. 59 1388 2016
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Hetero Components
(2, 9)
Info
All Hetero Components
1a: 2-(2-AZANYL-1,3-THIAZOL-4-YL)PYRID... (5UPa)
1b: 2-(2-AZANYL-1,3-THIAZOL-4-YL)PYRID... (5UPb)
1c: 2-(2-AZANYL-1,3-THIAZOL-4-YL)PYRID... (5UPc)
1d: 2-(2-AZANYL-1,3-THIAZOL-4-YL)PYRID... (5UPd)
2a: DIMETHYL SULFOXIDE (DMSa)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
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Label:
No.
Name
Count
Type
Full Name
1
5UP
1
Ligand/Ion
2-(2-AZANYL-1,3-THIAZOL-4-YL)PYRIDINE-4-CARBOXAMIDE
2
DMS
-1
Ligand/Ion
DIMETHYL SULFOXIDE
3
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
4
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(11, 11)
Info
All Sites
01: AF3 (SOFTWARE)
02: AF4 (SOFTWARE)
03: AF5 (SOFTWARE)
04: AF6 (SOFTWARE)
05: AF7 (SOFTWARE)
06: AF8 (SOFTWARE)
07: AF9 (SOFTWARE)
08: AG1 (SOFTWARE)
09: AG2 (SOFTWARE)
10: AG3 (SOFTWARE)
11: AG4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
01
AF3
SOFTWARE
HIS D:188 , GLU D:190 , HIS D:276 , 5UP D:403
binding site for residue ZN D 401
02
AF4
SOFTWARE
CYS D:234 , HIS D:240 , CYS D:306 , CYS D:308
binding site for residue ZN D 402
03
AF5
SOFTWARE
TYR D:132 , PHE D:185 , HIS D:188 , GLU D:190 , ASN D:198 , LYS D:206 , TRP D:208 , HIS D:276 , ZN D:401 , HOH D:528 , HOH D:541
binding site for residue 5UP D 403
04
AF6
SOFTWARE
GLU D:235 , ALA D:236 , PHE D:237 , LEU D:238
binding site for residue EDO D 404
05
AF7
SOFTWARE
THR D:83 , SER D:230 , HIS D:240 , THR D:243
binding site for residue EDO D 405
06
AF8
SOFTWARE
TRP D:122 , LEU D:248 , HOH D:549
binding site for residue EDO D 406
07
AF9
SOFTWARE
SER D:11 , ALA D:12 , PRO D:212 , PHE D:257 , EDO D:409
binding site for residue EDO D 407
08
AG1
SOFTWARE
PRO D:10 , SER D:11 , ALA D:12 , GLU D:214 , HIS D:215
binding site for residue EDO D 408
09
AG2
SOFTWARE
PHE D:257 , EDO D:407 , HOH D:519 , HOH D:529
binding site for residue EDO D 409
10
AG3
SOFTWARE
GLY D:170 , TYR D:177 , GLU D:190 , SER D:196 , SER D:288 , THR D:289 , ASN D:290
binding site for residue EDO D 410
11
AG4
SOFTWARE
GLU D:23 , ARG D:29 , TYR D:30
binding site for residue EDO D 411
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SAPs(SNPs)/Variants
(0, 0)
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Chain D
Asymmetric Unit 1
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Asym.Unit (483 KB)
Header - Asym.Unit
Biol.Unit 1 (120 KB)
Header - Biol.Unit 1
Biol.Unit 2 (123 KB)
Header - Biol.Unit 2
Biol.Unit 3 (123 KB)
Header - Biol.Unit 3
Biol.Unit 4 (123 KB)
Header - Biol.Unit 4
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