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5F37
Asym. Unit
Info
Asym.Unit (499 KB)
Biol.Unit 1 (124 KB)
Biol.Unit 2 (128 KB)
Biol.Unit 3 (124 KB)
Biol.Unit 4 (128 KB)
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Title
:
CRYSTAL STRUCTURE OF HUMAN KDM4A IN COMPLEX WITH COMPOUND 58
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
:
2.22
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
(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
[
close entry info
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Hetero Components
(4, 60)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
1b: DIMETHYL SULFOXIDE (DMSb)
1c: DIMETHYL SULFOXIDE (DMSc)
1d: DIMETHYL SULFOXIDE (DMSd)
1e: DIMETHYL SULFOXIDE (DMSe)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2ae: 1,2-ETHANEDIOL (EDOae)
2af: 1,2-ETHANEDIOL (EDOaf)
2ag: 1,2-ETHANEDIOL (EDOag)
2ah: 1,2-ETHANEDIOL (EDOah)
2ai: 1,2-ETHANEDIOL (EDOai)
2aj: 1,2-ETHANEDIOL (EDOaj)
2ak: 1,2-ETHANEDIOL (EDOak)
2al: 1,2-ETHANEDIOL (EDOal)
2am: 1,2-ETHANEDIOL (EDOam)
2an: 1,2-ETHANEDIOL (EDOan)
2ao: 1,2-ETHANEDIOL (EDOao)
2ap: 1,2-ETHANEDIOL (EDOap)
2aq: 1,2-ETHANEDIOL (EDOaq)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: 3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE (N5Ja)
3b: 3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE (N5Jb)
3c: 3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE (N5Jc)
3d: 3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE (N5Jd)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
5
Ligand/Ion
DIMETHYL SULFOXIDE
2
EDO
43
Ligand/Ion
1,2-ETHANEDIOL
3
N5J
4
Ligand/Ion
3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
4
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(60, 60)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
35: AF8 (SOFTWARE)
36: AF9 (SOFTWARE)
37: AG1 (SOFTWARE)
38: AG2 (SOFTWARE)
39: AG3 (SOFTWARE)
40: AG4 (SOFTWARE)
41: AG5 (SOFTWARE)
42: AG6 (SOFTWARE)
43: AG7 (SOFTWARE)
44: AG8 (SOFTWARE)
45: AG9 (SOFTWARE)
46: AH1 (SOFTWARE)
47: AH2 (SOFTWARE)
48: AH3 (SOFTWARE)
49: AH4 (SOFTWARE)
50: AH5 (SOFTWARE)
51: AH6 (SOFTWARE)
52: AH7 (SOFTWARE)
53: AH8 (SOFTWARE)
54: AH9 (SOFTWARE)
55: AI1 (SOFTWARE)
56: AI2 (SOFTWARE)
57: AI3 (SOFTWARE)
58: AI4 (SOFTWARE)
59: AI5 (SOFTWARE)
60: AI6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:188 , GLU A:190 , HIS A:276 , N5J A:403 , HOH A:504 , HOH A:524
binding site for residue ZN A 401
02
AC2
SOFTWARE
CYS A:234 , HIS A:240 , CYS A:306 , CYS A:308
binding site for residue ZN A 402
03
AC3
SOFTWARE
TYR A:132 , TYR A:177 , PHE A:185 , HIS A:188 , ASN A:198 , LYS A:206 , TRP A:208 , LYS A:241 , HIS A:276 , ZN A:401 , HOH A:504
binding site for residue N5J A 403
04
AC4
SOFTWARE
GLY A:170 , GLU A:190 , SER A:288 , THR A:289 , ASN A:290 , HOH A:524
binding site for residue EDO A 404
05
AC5
SOFTWARE
THR A:83 , SER A:230 , HIS A:240 , MET A:242 , THR A:243
binding site for residue EDO A 405
06
AC6
SOFTWARE
LEU A:65 , GLY A:138 , THR A:139
binding site for residue EDO A 406
07
AC7
SOFTWARE
ILE A:150 , GLY A:151 , LEU A:153 , ASN A:290 , HOH A:506
binding site for residue EDO A 407
08
AC8
SOFTWARE
ASN A:9 , PRO A:10 , SER A:11 , ALA A:12
binding site for residue EDO A 408
09
AC9
SOFTWARE
SER A:11 , ALA A:12 , ARG A:13 , PRO A:212 , PHE A:257 , ASP A:258 , HOH A:546
binding site for residue EDO A 409
10
AD1
SOFTWARE
ALA A:134 , ASP A:135 , LYS A:241 , HOH A:503
binding site for residue EDO A 410
11
AD2
SOFTWARE
PRO A:50 , LYS A:51 , TRP A:53 , TYR A:199 , EDO A:415
binding site for residue EDO A 411
12
AD3
SOFTWARE
GLU A:235 , ALA A:236 , PHE A:237 , LEU A:238
binding site for residue EDO A 412
13
AD4
SOFTWARE
LYS A:251 , GLY A:254 , ILE A:255 , PHE A:257 , EDO A:414
binding site for residue EDO A 413
14
AD5
SOFTWARE
PHE A:257 , EDO A:413
binding site for residue EDO A 414
15
AD6
SOFTWARE
HIS A:201 , EDO A:411
binding site for residue EDO A 415
16
AD7
SOFTWARE
TYR A:59 , ARG A:98 , PHE A:202
binding site for residue DMS A 416
17
AD8
SOFTWARE
LYS A:54 , PRO A:55 , ARG A:56 , ALA A:57 , GLU A:142 , HIS A:144
binding site for residue DMS A 417
18
AD9
SOFTWARE
HIS B:188 , GLU B:190 , HIS B:276 , N5J B:403 , HOH B:540 , HOH B:545
binding site for residue ZN B 401
19
AE1
SOFTWARE
CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308
binding site for residue ZN B 402
20
AE2
SOFTWARE
TYR B:132 , TYR B:177 , PHE B:185 , HIS B:188 , ASN B:198 , LYS B:206 , TRP B:208 , LYS B:241 , HIS B:276 , ZN B:401 , HOH B:545
binding site for residue N5J B 403
21
AE3
SOFTWARE
GLY B:170 , GLU B:190 , SER B:288 , THR B:289 , HOH B:540
binding site for residue EDO B 404
22
AE4
SOFTWARE
ASN B:9 , PRO B:10 , SER B:11
binding site for residue EDO B 405
23
AE5
SOFTWARE
PRO B:10 , ALA B:12 , GLU B:214 , HIS B:215
binding site for residue EDO B 406
24
AE6
SOFTWARE
SER B:11 , ALA B:12 , ARG B:13 , PRO B:212 , PHE B:257 , ASP B:258 , HOH B:578
binding site for residue EDO B 407
25
AE7
SOFTWARE
PRO B:256 , PHE B:257 , EDO B:417
binding site for residue EDO B 408
26
AE8
SOFTWARE
LEU B:65 , GLY B:138 , THR B:139
binding site for residue EDO B 409
27
AE9
SOFTWARE
THR B:83 , PHE B:227 , SER B:230 , HIS B:240 , THR B:243
binding site for residue EDO B 410
28
AF1
SOFTWARE
ILE B:150 , GLY B:151 , ARG B:152 , LEU B:153 , ASN B:290 , HOH B:520
binding site for residue EDO B 411
29
AF2
SOFTWARE
LEU B:8 , ASN B:9 , GLN B:37
binding site for residue EDO B 412
30
AF3
SOFTWARE
GLU B:23 , ARG B:29 , HOH B:583
binding site for residue EDO B 413
31
AF4
SOFTWARE
ASN B:86 , ALA B:134 , ASP B:135 , SER B:184 , LYS B:241 , HOH B:507 , HOH B:628
binding site for residue EDO B 414
32
AF5
SOFTWARE
HIS B:188 , THR B:189 , ASP B:191 , ARG B:239 , HOH B:598
binding site for residue EDO B 415
33
AF6
SOFTWARE
LYS B:224 , GLU B:235 , ALA B:236 , PHE B:237 , LEU B:238 , HOH B:591
binding site for residue EDO B 416
34
AF7
SOFTWARE
LYS B:251 , GLY B:254 , ILE B:255 , PRO B:256 , EDO B:408
binding site for residue EDO B 417
35
AF8
SOFTWARE
GLN B:88
binding site for residue DMS B 418
36
AF9
SOFTWARE
HIS C:188 , GLU C:190 , HIS C:276 , N5J C:403 , HOH C:536 , HOH C:561
binding site for residue ZN C 401
37
AG1
SOFTWARE
CYS C:234 , HIS C:240 , CYS C:306 , CYS C:308
binding site for residue ZN C 402
38
AG2
SOFTWARE
TYR C:132 , TYR C:177 , PHE C:185 , HIS C:188 , LYS C:206 , LYS C:241 , HIS C:276 , ZN C:401 , EDO C:410 , HOH C:536 , HOH C:561
binding site for residue N5J C 403
39
AG3
SOFTWARE
GLY C:170 , TYR C:177 , GLU C:190 , SER C:288 , THR C:289 , HOH C:536
binding site for residue EDO C 404
40
AG4
SOFTWARE
THR C:83 , PHE C:227 , THR C:243
binding site for residue EDO C 405
41
AG5
SOFTWARE
GLY C:138 , THR C:139
binding site for residue EDO C 406
42
AG6
SOFTWARE
SER C:11 , ALA C:12 , ARG C:13 , PRO C:212 , PHE C:257 , ASP C:258 , HOH C:531 , HOH C:556
binding site for residue EDO C 407
43
AG7
SOFTWARE
GLU C:23 , TYR C:30 , HOH C:527
binding site for residue EDO C 408
44
AG8
SOFTWARE
ILE C:150 , GLY C:151 , ARG C:152 , LEU C:153 , ASN C:290 , HOH C:511
binding site for residue EDO C 409
45
AG9
SOFTWARE
ALA C:134 , ASP C:135 , LYS C:241 , N5J C:403 , HOH C:515
binding site for residue EDO C 410
46
AH1
SOFTWARE
TYR C:59 , ILE C:62 , ARG C:98
binding site for residue DMS C 411
47
AH2
SOFTWARE
HIS D:188 , GLU D:190 , HIS D:276 , N5J D:403 , HOH D:528 , HOH D:530
binding site for residue ZN D 401
48
AH3
SOFTWARE
CYS D:234 , HIS D:240 , CYS D:306 , CYS D:308
binding site for residue ZN D 402
49
AH4
SOFTWARE
TYR D:132 , TYR D:177 , PHE D:185 , HIS D:188 , ASN D:198 , LYS D:206 , TRP D:208 , LYS D:241 , HIS D:276 , ZN D:401 , HOH D:528 , HOH D:530
binding site for residue N5J D 403
50
AH5
SOFTWARE
LYS D:224 , GLU D:235 , ALA D:236 , PHE D:237 , LEU D:238 , HOH D:519 , HOH D:601
binding site for residue EDO D 404
51
AH6
SOFTWARE
HIS D:201
binding site for residue EDO D 405
52
AH7
SOFTWARE
THR D:83 , PHE D:227 , SER D:230 , PHE D:237 , THR D:243 , HOH D:598
binding site for residue EDO D 406
53
AH8
SOFTWARE
SER D:11 , ALA D:12 , ARG D:13 , PRO D:212 , PHE D:257 , ASP D:258 , HOH D:564
binding site for residue EDO D 407
54
AH9
SOFTWARE
SER D:11 , GLU D:214 , HIS D:215 , HOH D:623
binding site for residue EDO D 408
55
AI1
SOFTWARE
LYS D:251 , GLY D:254 , ILE D:255 , EDO D:411
binding site for residue EDO D 409
56
AI2
SOFTWARE
GLU A:161 , LYS A:162 , ARG D:56 , ASP D:61
binding site for residue EDO D 410
57
AI3
SOFTWARE
PHE D:257 , EDO D:409
binding site for residue EDO D 411
58
AI4
SOFTWARE
GLU D:23 , ARG D:29 , PHE D:353 , HOH D:520
binding site for residue EDO D 412
59
AI5
SOFTWARE
ALA D:134 , ASP D:135 , SER D:184 , LYS D:241 , HOH D:545 , HOH D:560
binding site for residue EDO D 413
60
AI6
SOFTWARE
TYR D:59 , ARG D:98
binding site for residue DMS D 414
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SAPs(SNPs)/Variants
(0, 0)
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