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2XNO
Asym. Unit
Info
Asym.Unit (98 KB)
Biol.Unit 1 (93 KB)
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(1)
Title
:
STRUCTURE OF NEK2 BOUND TO CCT243779
Authors
:
C. Mas-Droux, R. Bayliss
Date
:
05 Aug 10 (Deposition) - 30 Mar 11 (Release) - 30 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.98
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Transferase, Centrosome, Mitosis, Cell Cycle
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Solanki, P. Innocenti, C. Mas-Droux, K. Boxall, C. Barillari, R. L. Van Montfort, G. W. Aherne, R. Bayliss, S. Hoelder
Benzimidazole Inhibitors Induce A Dfg-Out Conformation Of Never In Mitosis Gene A-Related Kinase 2 (Nek2) Without Binding To The Back Pocket And Reveal A Nonlinear Structure-Activity Relationship.
J. Med. Chem. V. 54 1626 2011
[
close entry info
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Hetero Components
(5, 16)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: DIMETHYL SULFOXIDE (DMSa)
3a: 5-{6-[(1-METHYLPIPERIDIN-4-YL)OXY]... (ED8a)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
4c: 1,2-ETHANEDIOL (EDOc)
4d: 1,2-ETHANEDIOL (EDOd)
4e: 1,2-ETHANEDIOL (EDOe)
4f: 1,2-ETHANEDIOL (EDOf)
4g: 1,2-ETHANEDIOL (EDOg)
4h: 1,2-ETHANEDIOL (EDOh)
4i: 1,2-ETHANEDIOL (EDOi)
4j: 1,2-ETHANEDIOL (EDOj)
4k: 1,2-ETHANEDIOL (EDOk)
5a: GLYCEROL (GOLa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
DMS
1
Ligand/Ion
DIMETHYL SULFOXIDE
3
ED8
1
Ligand/Ion
5-{6-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-3-{[2-(TRIFLUOROMETHYL)BENZYL]OXY}THIOPHENE-2-CARBOXAMIDE
4
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
5
GOL
1
Ligand/Ion
GLYCEROL
[
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Sites
(15, 15)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:14 , GLY A:15 , CYS A:22 , LYS A:37 , GLU A:87 , TYR A:88 , CYS A:89 , ASP A:93 , SER A:96 , ALA A:145 , PHE A:148 , GLY A:158 , ASP A:159 , EDO A:1294 , HOH A:2034 , HOH A:2194
BINDING SITE FOR RESIDUE ED8 A1280
02
AC2
SOFTWARE
GLU A:110 , ARG A:239 , HOH A:2064
BINDING SITE FOR RESIDUE CL A1282
03
AC3
SOFTWARE
LEU A:11 , LYS A:152 , GLN A:153 , HOH A:2190 , HOH A:2195 , HOH A:2196
BINDING SITE FOR RESIDUE EDO A1283
04
AC4
SOFTWARE
TYR A:181 , GLU A:208 , PRO A:214 , HOH A:2197
BINDING SITE FOR RESIDUE EDO A1284
05
AC5
SOFTWARE
GLU A:195 , LYS A:196 , SER A:261 , VAL A:262 , HOH A:2198
BINDING SITE FOR RESIDUE EDO A1285
06
AC6
SOFTWARE
ARG A:234 , ARG A:235 , TYR A:238 , LEU A:266 , EDO A:1289 , EDO A:1290 , HOH A:2199
BINDING SITE FOR RESIDUE EDO A1286
07
AC7
SOFTWARE
TYR A:238 , ASP A:242 , HOH A:2104 , HOH A:2202 , HOH A:2203
BINDING SITE FOR RESIDUE EDO A1287
08
AC8
SOFTWARE
ILE A:247 , GLU A:264 , ASN A:268
BINDING SITE FOR RESIDUE EDO A1288
09
AC9
SOFTWARE
ARG A:234 , ARG A:235 , TYR A:238 , LEU A:266 , ILE A:271 , LEU A:272 , GLU A:273 , HIS A:276 , EDO A:1286
BINDING SITE FOR RESIDUE EDO A1289
10
BC1
SOFTWARE
TYR A:207 , ALA A:211 , ARG A:235 , ILE A:236 , EDO A:1286 , HOH A:2129
BINDING SITE FOR RESIDUE EDO A1290
11
BC2
SOFTWARE
ASP A:242 , GLU A:246 , HIS A:277 , HIS A:279 , HOH A:2154 , HOH A:2205
BINDING SITE FOR RESIDUE EDO A1291
12
BC3
SOFTWARE
ARG A:140 , ASP A:159 , PHE A:160 , HOH A:2114 , HOH A:2206 , HOH A:2207
BINDING SITE FOR RESIDUE GOL A1292
13
BC4
SOFTWARE
PRO A:65 , ASN A:154 , LYS A:156 , HIS A:277 , HIS A:279
BINDING SITE FOR RESIDUE DMS A1293
14
BC5
SOFTWARE
ASP A:159 , ED8 A:1280
BINDING SITE FOR RESIDUE EDO A1294
15
BC6
SOFTWARE
PHE A:160
BINDING SITE FOR RESIDUE EDO A1295
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ST (A:140-149)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
NEK2_HUMAN
137-149
1
A:140-149
[
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]
Exons
(6, 6)
Info
All Exons
Exon 1.1a (A:3-32)
Exon 1.2 (A:33-105)
Exon 1.3 (A:105-185 (gaps))
Exon 1.4a (A:186-213 (gaps))
Exon 1.5a (A:213-255)
Exon 1.6b (A:256-279)
View:
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All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4a
5: Boundary 1.4a/1.5a
6: Boundary 1.5a/1.6b
7: Boundary 1.6b/1.7a
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
1.1a
ENST00000366999
1a
ENSE00001443207
chr1:
211848960-211848726
235
NEK2_HUMAN
1-32
32
1
A:3-32
30
1.2
ENST00000366999
2
ENSE00001010392
chr1:
211847855-211847638
218
NEK2_HUMAN
33-105
73
1
A:33-105
73
1.3
ENST00000366999
3
ENSE00001167194
chr1:
211847065-211846825
241
NEK2_HUMAN
105-185
81
1
A:105-185 (gaps)
81
1.4a
ENST00000366999
4a
ENSE00001010393
chr1:
211844626-211844544
83
NEK2_HUMAN
186-213
28
1
A:186-213 (gaps)
28
1.5a
ENST00000366999
5a
ENSE00001010397
chr1:
211843749-211843623
127
NEK2_HUMAN
213-255
43
1
A:213-255
43
1.6b
ENST00000366999
6b
ENSE00001010396
chr1:
211842674-211842455
220
NEK2_HUMAN
256-329
74
1
A:256-279
24
1.7a
ENST00000366999
7a
ENSE00000792201
chr1:
211840573-211840448
126
NEK2_HUMAN
329-371
43
0
-
-
1.8b
ENST00000366999
8b
ENSE00001443206
chr1:
211836994-211836114
881
NEK2_HUMAN
371-445
75
0
-
-
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2xnoa_ (A:)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Protein kinase-like (PK-like)
(2589)
Superfamily
:
Protein kinase-like (PK-like)
(2589)
Family
:
Protein kinases, catalytic subunit
(1977)
Protein domain
:
automated matches
(542)
Human (Homo sapiens) [TaxId: 9606]
(452)
1a
d2xnoa_
A:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Pkinase_2xnoA01 (A:8-271)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
1a
Pkinase-2xnoA01
A:8-271
[
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]
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Chain A
Asymmetric Unit 1
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