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3RJW
Asym. Unit
Info
Asym.Unit (191 KB)
Biol.Unit 1 (183 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HISTONE LYSINE METHYLTRANSFERASE G9A WITH AN INHIBITOR
Authors
:
A. Dong, G. A. Wasney, W. Tempel, F. Liu, D. Barsyte, A. Allali-Hassani, I. Chau, T. Hajian, G. Senisterra, N. Chavda, K. Arora, A. Siarheyeva, D. B. Kireev, J. M. Herold, A. Bochkarev, C. Bountra, J. Weigelt, A. M. E S. V. Frye, C. H. Arrowsmith, P. J. Brown, J. Jin, M. Vedadi, Structural Consortium (Sgc)
Date
:
15 Apr 11 (Deposition) - 04 May 11 (Release) - 03 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.56
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Chemical Probe, Methyltransferase Inhibitor, Structural Genomics Consortium, Sgc, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Vedadi, D. Barsyte-Lovejoy, F. Liu, S. Rival-Gervier, A. Allali-Hassani, V. Labrie, T. J. Wigle, P. A. Dimaggio, G. A. Wasney A. Siarheyeva, A. Dong, W. Tempel, S. C. Wang, X. Chen, I. Chau, T. J. Mangano, X. P. Huang, C. D. Simpson, S. G. Pattenden, J. L. Norris, D. B. Kireev, A. Tripathy, A. Edwards, B. L. Roth, W. P. Janzen, B. A. Garcia, A. Petronis, J. Ellis, P. J. Brown, S. V. Frye, C. H. Arrowsmith, J. Jin
A Chemical Probe Selectively Inhibits G9A And Glp Methyltransferase Activity In Cells.
Nat. Chem. Biol. V. 7 566 2011
[
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Hetero Components
(4, 41)
Info
All Hetero Components
1a: 2-CYCLOHEXYL-6-METHOXY-N-[1-(1-MET... (CIQa)
1b: 2-CYCLOHEXYL-6-METHOXY-N-[1-(1-MET... (CIQb)
2a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
2b: S-ADENOSYL-L-HOMOCYSTEINE (SAHb)
3a: UNKNOWN ATOM OR ION (UNXa)
3aa: UNKNOWN ATOM OR ION (UNXaa)
3ab: UNKNOWN ATOM OR ION (UNXab)
3ac: UNKNOWN ATOM OR ION (UNXac)
3b: UNKNOWN ATOM OR ION (UNXb)
3c: UNKNOWN ATOM OR ION (UNXc)
3d: UNKNOWN ATOM OR ION (UNXd)
3e: UNKNOWN ATOM OR ION (UNXe)
3f: UNKNOWN ATOM OR ION (UNXf)
3g: UNKNOWN ATOM OR ION (UNXg)
3h: UNKNOWN ATOM OR ION (UNXh)
3i: UNKNOWN ATOM OR ION (UNXi)
3j: UNKNOWN ATOM OR ION (UNXj)
3k: UNKNOWN ATOM OR ION (UNXk)
3l: UNKNOWN ATOM OR ION (UNXl)
3m: UNKNOWN ATOM OR ION (UNXm)
3n: UNKNOWN ATOM OR ION (UNXn)
3o: UNKNOWN ATOM OR ION (UNXo)
3p: UNKNOWN ATOM OR ION (UNXp)
3q: UNKNOWN ATOM OR ION (UNXq)
3r: UNKNOWN ATOM OR ION (UNXr)
3s: UNKNOWN ATOM OR ION (UNXs)
3t: UNKNOWN ATOM OR ION (UNXt)
3u: UNKNOWN ATOM OR ION (UNXu)
3v: UNKNOWN ATOM OR ION (UNXv)
3w: UNKNOWN ATOM OR ION (UNXw)
3x: UNKNOWN ATOM OR ION (UNXx)
3y: UNKNOWN ATOM OR ION (UNXy)
3z: UNKNOWN ATOM OR ION (UNXz)
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
CIQ
2
Ligand/Ion
2-CYCLOHEXYL-6-METHOXY-N-[1-(1-METHYLETHYL)PIPERIDIN-4-YL]-7-(3-PYRROLIDIN-1-YLPROPOXY)QUINAZOLIN-4-AMINE
2
SAH
2
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
3
UNX
29
Ligand/Ion
UNKNOWN ATOM OR ION
4
ZN
8
Ligand/Ion
ZINC ION
[
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Sites
(12, 12)
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: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:974 , CYS A:987 , CYS A:1017 , CYS A:1021
BINDING SITE FOR RESIDUE ZN A 1394
02
AC2
SOFTWARE
CYS A:980 , CYS A:1017 , CYS A:1023 , CYS A:1027
BINDING SITE FOR RESIDUE ZN A 1395
03
AC3
SOFTWARE
CYS A:974 , CYS A:976 , CYS A:980 , CYS A:985
BINDING SITE FOR RESIDUE ZN A 1396
04
AC4
SOFTWARE
CYS A:1115 , CYS A:1168 , CYS A:1170 , CYS A:1175
BINDING SITE FOR RESIDUE ZN A 1397
05
AC5
SOFTWARE
HOH A:2 , MET A:1048 , TRP A:1050 , SER A:1084 , TYR A:1085 , ARG A:1109 , PHE A:1110 , ASN A:1112 , HIS A:1113 , TYR A:1154 , PHE A:1158 , PHE A:1166 , THR A:1167 , CYS A:1168 , GLN A:1169
BINDING SITE FOR RESIDUE SAH A 1198
06
AC6
SOFTWARE
TYR A:1067 , ASP A:1074 , ALA A:1077 , ASP A:1078 , ARG A:1080 , ASP A:1083 , SER A:1084 , LEU A:1086 , ASP A:1088 , TYR A:1154 , PHE A:1158 , ILE A:1161
BINDING SITE FOR RESIDUE CIQ A 2000
07
AC7
SOFTWARE
CYS B:974 , CYS B:987 , CYS B:1017 , CYS B:1021
BINDING SITE FOR RESIDUE ZN B 1394
08
AC8
SOFTWARE
CYS B:980 , CYS B:1017 , CYS B:1023 , CYS B:1027
BINDING SITE FOR RESIDUE ZN B 1395
09
AC9
SOFTWARE
CYS B:974 , CYS B:976 , CYS B:980 , CYS B:985
BINDING SITE FOR RESIDUE ZN B 1396
10
BC1
SOFTWARE
CYS B:1115 , CYS B:1168 , CYS B:1170 , CYS B:1175
BINDING SITE FOR RESIDUE ZN B 1397
11
BC2
SOFTWARE
MET B:1048 , TRP B:1050 , SER B:1084 , TYR B:1085 , ARG B:1109 , PHE B:1110 , ASN B:1112 , HIS B:1113 , TYR B:1154 , PHE B:1158 , PHE B:1166 , THR B:1167 , CYS B:1168 , GLN B:1169 , HOH B:1197
BINDING SITE FOR RESIDUE SAH B 1198
12
BC3
SOFTWARE
TYR B:1067 , ASP B:1074 , ALA B:1077 , ASP B:1078 , ARG B:1080 , ASP B:1083 , SER B:1084 , LEU B:1086 , ASP B:1088 , TYR B:1154 , PHE B:1158
BINDING SITE FOR RESIDUE CIQ B 2000
[
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]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_027974 (Y1165F, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_027974
Y
1165
F
EHMT2_HUMAN
Polymorphism
13919
A/B
Y
1165
F
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PRE_SET (A:972-1035,B:972-1035)
2: SET (A:1038-1155,B:1038-1155)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PRE_SET
PS50867
Pre-SET domain profile.
EHMT2_HUMAN
972-1035
2
A:972-1035
B:972-1035
2
SET
PS50280
SET domain profile.
EHMT2_HUMAN
1038-1155
2
A:1038-1155
B:1038-1155
[
close PROSITE info
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Exons
(8, 16)
Info
All Exons
Exon 1.78t (A:918-924 | B:921-924)
Exon 1.79h (A:924-972 | B:924-972)
Exon 1.80b (A:973-998 | B:973-998)
Exon 1.80c (A:999-1037 | B:999-1037)
Exon 1.80d (A:1037-1066 | B:1037-1066)
Exon 1.83d (A:1066-1092 | B:1066-1091)
Exon 1.84b (A:1093-1151 | B:1095-1151)
Exon 1.86b (A:1151-1187 (gaps) | B:1151-1193)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.78q/1.78t
2: Boundary 1.78t/1.79h
3: Boundary 1.79h/1.80b
4: Boundary 1.80b/1.80c
5: Boundary 1.80c/1.80d
6: Boundary 1.80d/1.83d
7: Boundary 1.83d/1.84b
8: Boundary 1.84b/1.86b
9: Boundary 1.86b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.62b
ENST00000383373
62b
ENSE00001868068
HSCHR6_MHC_QBL:31855870-31855807
64
EHMT2_HUMAN
1-14
14
0
-
-
1.64e
ENST00000383373
64e
ENSE00001706010
HSCHR6_MHC_QBL:31855160-31855094
67
EHMT2_HUMAN
15-37
23
0
-
-
1.65a
ENST00000383373
65a
ENSE00001599572
HSCHR6_MHC_QBL:31854995-31854777
219
EHMT2_HUMAN
37-110
74
0
-
-
1.65e
ENST00000383373
65e
ENSE00001775009
HSCHR6_MHC_QBL:31854687-31854434
254
EHMT2_HUMAN
110-194
85
0
-
-
1.68i
ENST00000383373
68i
ENSE00001728907
HSCHR6_MHC_QBL:31851081-31850997
85
EHMT2_HUMAN
195-223
29
0
-
-
1.68j
ENST00000383373
68j
ENSE00001788063
HSCHR6_MHC_QBL:31850905-31850865
41
EHMT2_HUMAN
223-236
14
0
-
-
1.68m
ENST00000383373
68m
ENSE00001596027
HSCHR6_MHC_QBL:31850733-31850578
156
EHMT2_HUMAN
237-288
52
0
-
-
1.72f
ENST00000383373
72f
ENSE00001688918
HSCHR6_MHC_QBL:31847773-31847639
135
EHMT2_HUMAN
289-333
45
0
-
-
1.73
ENST00000383373
73
ENSE00001675787
HSCHR6_MHC_QBL:31847513-31847399
115
EHMT2_HUMAN
334-372
39
0
-
-
1.74a
ENST00000383373
74a
ENSE00001783494
HSCHR6_MHC_QBL:31847241-31847140
102
EHMT2_HUMAN
372-406
35
0
-
-
1.74e
ENST00000383373
74e
ENSE00001756695
HSCHR6_MHC_QBL:31846918-31846770
149
EHMT2_HUMAN
406-455
50
0
-
-
1.74g
ENST00000383373
74g
ENSE00001659464
HSCHR6_MHC_QBL:31846677-31846534
144
EHMT2_HUMAN
456-503
48
0
-
-
1.75d
ENST00000383373
75d
ENSE00001776567
HSCHR6_MHC_QBL:31846447-31846212
236
EHMT2_HUMAN
504-582
79
0
-
-
1.75e
ENST00000383373
75e
ENSE00001616295
HSCHR6_MHC_QBL:31846132-31845950
183
EHMT2_HUMAN
582-643
62
0
-
-
1.75f
ENST00000383373
75f
ENSE00001626945
HSCHR6_MHC_QBL:31845830-31845748
83
EHMT2_HUMAN
643-671
29
0
-
-
1.76b
ENST00000383373
76b
ENSE00001661306
HSCHR6_MHC_QBL:31845272-31845166
107
EHMT2_HUMAN
671-706
36
0
-
-
1.76d
ENST00000383373
76d
ENSE00001674057
HSCHR6_MHC_QBL:31845068-31844946
123
EHMT2_HUMAN
707-747
41
0
-
-
1.77b
ENST00000383373
77b
ENSE00001779819
HSCHR6_MHC_QBL:31844853-31844752
102
EHMT2_HUMAN
748-781
34
0
-
-
1.78k
ENST00000383373
78k
ENSE00001761048
HSCHR6_MHC_QBL:31843187-31843083
105
EHMT2_HUMAN
782-816
35
0
-
-
1.78q
ENST00000383373
78q
ENSE00001617974
HSCHR6_MHC_QBL:31842970-31842816
155
EHMT2_HUMAN
817-868
52
0
-
-
1.78t
ENST00000383373
78t
ENSE00001680216
HSCHR6_MHC_QBL:31842730-31842563
168
EHMT2_HUMAN
868-924
57
2
A:918-924
B:921-924
7
4
1.79h
ENST00000383373
79h
ENSE00001760590
HSCHR6_MHC_QBL:31842121-31841977
145
EHMT2_HUMAN
924-972
49
2
A:924-972
B:924-972
49
49
1.80b
ENST00000383373
80b
ENSE00001750625
HSCHR6_MHC_QBL:31841610-31841533
78
EHMT2_HUMAN
973-998
26
2
A:973-998
B:973-998
26
26
1.80c
ENST00000383373
80c
ENSE00001653707
HSCHR6_MHC_QBL:31841180-31841065
116
EHMT2_HUMAN
999-1037
39
2
A:999-1037
B:999-1037
39
39
1.80d
ENST00000383373
80d
ENSE00001641889
HSCHR6_MHC_QBL:31840956-31840870
87
EHMT2_HUMAN
1037-1066
30
2
A:1037-1066
B:1037-1066
30
30
1.83d
ENST00000383373
83d
ENSE00001692473
HSCHR6_MHC_QBL:31839264-31839186
79
EHMT2_HUMAN
1066-1092
27
2
A:1066-1092
B:1066-1091
27
26
1.84b
ENST00000383373
84b
ENSE00001740322
HSCHR6_MHC_QBL:31839020-31838845
176
EHMT2_HUMAN
1093-1151
59
2
A:1093-1151
B:1095-1151
59
57
1.86b
ENST00000383373
86b
ENSE00001647961
HSCHR6_MHC_QBL:31838436-31837931
506
EHMT2_HUMAN
1151-1210
60
2
A:1151-1187 (gaps)
B:1151-1193
37
43
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3rjwa_ (A:)
1b: SCOP_d3rjwb_ (B:)
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Class
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All beta proteins
(24004)
Fold
:
beta-clip
(280)
Superfamily
:
SET domain
(44)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Human (Homo sapiens) [TaxId: 9606]
(11)
1a
d3rjwa_
A:
1b
d3rjwb_
B:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Pre_SET_3rjwB01 (B:925-1030)
1b: PFAM_Pre_SET_3rjwB02 (B:925-1030)
2a: PFAM_SET_3rjwB03 (B:1049-1155)
2b: PFAM_SET_3rjwB04 (B:1049-1155)
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Clan
:
no clan defined [family: Pre-SET]
(11)
Family
:
Pre-SET
(11)
Homo sapiens (Human)
(8)
1a
Pre-SET-3rjwB01
B:925-1030
1b
Pre-SET-3rjwB02
B:925-1030
Clan
:
no clan defined [family: SET]
(46)
Family
:
SET
(46)
Homo sapiens (Human)
(34)
2a
SET-3rjwB03
B:1049-1155
2b
SET-3rjwB04
B:1049-1155
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