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3R2B
Asym. Unit
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Asym.Unit (1.1 MB)
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Biol.Unit 12 (99 KB)
Biol.Unit 2 (98 KB)
Biol.Unit 3 (99 KB)
Biol.Unit 4 (98 KB)
Biol.Unit 5 (99 KB)
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Biol.Unit 9 (98 KB)
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(1)
Title
:
MK2 KINASE BOUND TO COMPOUND 5B
Authors
:
A. Oubrie, M. Van Zeeland, J. Versteegh
Date
:
14 Mar 11 (Deposition) - 25 May 11 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Biol. Unit 9: I (1x)
Biol. Unit 10: J (1x)
Biol. Unit 11: K (1x)
Biol. Unit 12: L (1x)
Keywords
:
Kinase Domain With Bound Inhibitor, Kinase Domain, Phosphotransferase, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Barf, A. Kaptein, S. Wilde, R. Heijden, R. Someren, D. Demont, C. Schultz-Fademrecht, J. Versteegh, M. Zeeland, N. Seegers, B. Kazemier, B. Kar, M. Hoek, J. Roos, H. Klop, R. Smeets, C. Hofstra, J. Hornberg, A. Oubrie
Structure-Based Lead Identification Of Atp-Competitive Mk2 Inhibitors.
Bioorg. Med. Chem. Lett. V. 21 3818 2011
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: 2'-[2-(1,3-BENZODIOXOL-5-YL)PYRIMI... (05Ba)
1b: 2'-[2-(1,3-BENZODIOXOL-5-YL)PYRIMI... (05Bb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
05B
2
Ligand/Ion
2'-[2-(1,3-BENZODIOXOL-5-YL)PYRIMIDIN-4-YL]-5',6'-DIHYDROSPIRO[PIPERIDINE-4,7'-PYRROLO[3,2-C]PYRIDIN]-4'(1'H)-ONE
[
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:70 , LEU A:72 , VAL A:78 , ALA A:91 , LYS A:93 , GLU A:139 , CYS A:140 , LEU A:141 , GLU A:190 , ASN A:191 , LEU A:193 , ASP A:207
BINDING SITE FOR RESIDUE 05B A 1000
2
AC2
SOFTWARE
LEU B:72 , VAL B:78 , ALA B:91 , LYS B:93 , GLU B:139 , LEU B:141 , ASP B:142 , ASN B:191 , LEU B:193 , THR B:206 , ASP B:207
BINDING SITE FOR RESIDUE 05B B 1000
[
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SAPs(SNPs)/Variants
(1, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_040753 (A173G, chain A/B/C/D/E/F/G/H/I/J/K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_040753
A
173
G
MAPK2_HUMAN
Polymorphism
35671930
A/B/C/D/E/F/G/H/I/J/K/L
A
173
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(2, 24)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:70-93,B:70-93,C:70-93,D:70-93,E:...)
2: PROTEIN_KINASE_ST (A:182-194,B:182-194,C:182-194,D:18...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
MAPK2_HUMAN
70-93
12
A:70-93
B:70-93
C:70-93
D:70-93
E:70-93
F:70-93
G:70-93
H:70-93
I:70-93
J:70-93
K:70-93
L:70-93
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
MAPK2_HUMAN
182-194
12
A:182-194
B:182-194
C:182-194
D:182-194
E:182-194
F:182-194
G:182-194
H:182-194
I:182-194
J:182-194
K:182-194
L:182-194
[
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]
Exons
(9, 108)
Info
All Exons
Exon 1.1b (A:47-93 | B:47-93 | C:47-93 | D:47...)
Exon 1.2 (A:94-140 | B:94-140 | C:94-140 | D...)
Exon 1.3b (A:140-162 (gaps) | B:140-162 (gaps...)
Exon 1.4b (A:162-188 | B:162-188 | C:162-188 ...)
Exon 1.5 (A:189-231 (gaps) | B:189-231 (gaps...)
Exon 1.6 (A:231-256 (gaps) | B:231-256 (gaps...)
Exon 1.7 (A:256-298 (gaps) | B:256-298 (gaps...)
Exon 1.8b (A:298-326 | B:298-326 | C:298-326 ...)
Exon 1.9b (A:327-345 | B:327-345 | C:327-345 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2
03: Boundary 1.2/1.3b
04: Boundary 1.3b/1.4b
05: Boundary 1.4b/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8b
09: Boundary 1.8b/1.9b
10: Boundary 1.9b/1.9d
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
1.1b
ENST00000367103
1b
ENSE00001825387
chr1:
206858382-206858853
472
MAPK2_HUMAN
1-93
93
12
A:47-93
B:47-93
C:47-93
D:47-93
E:47-93
F:47-93
G:47-93
H:47-93
I:47-93
J:47-93
K:47-93
L:47-93
47
47
47
47
47
47
47
47
47
47
47
47
1.2
ENST00000367103
2
ENSE00001069545
chr1:
206902055-206902194
140
MAPK2_HUMAN
94-140
47
12
A:94-140
B:94-140
C:94-140
D:94-140
E:94-140
F:94-140
G:94-140
H:94-140
I:94-140
J:94-140
K:94-140
L:94-140
47
47
47
47
47
47
47
47
47
47
47
47
1.3b
ENST00000367103
3b
ENSE00001069547
chr1:
206902380-206902444
65
MAPK2_HUMAN
140-162
23
12
A:140-162 (gaps)
B:140-162 (gaps)
C:140-162 (gaps)
D:140-162 (gaps)
E:140-162 (gaps)
F:140-162 (gaps)
G:140-162 (gaps)
H:140-162 (gaps)
I:140-162 (gaps)
J:140-162 (gaps)
K:140-162 (gaps)
L:140-162 (gaps)
23
23
23
23
23
23
23
23
23
23
23
23
1.4b
ENST00000367103
4b
ENSE00001069548
chr1:
206902741-206902820
80
MAPK2_HUMAN
162-188
27
12
A:162-188
B:162-188
C:162-188
D:162-188
E:162-188
F:162-188
G:162-188
H:162-188
I:162-188
J:162-188
K:162-188
L:162-188
27
27
27
27
27
27
27
27
27
27
27
27
1.5
ENST00000367103
5
ENSE00001069551
chr1:
206903317-206903443
127
MAPK2_HUMAN
189-231
43
12
A:189-231 (gaps)
B:189-231 (gaps)
C:189-231 (gaps)
D:189-231 (gaps)
E:189-231 (gaps)
F:189-231 (gaps)
G:189-231 (gaps)
H:189-231 (gaps)
I:189-231 (gaps)
J:189-231 (gaps)
K:189-231 (gaps)
L:189-231 (gaps)
43
43
43
43
43
43
43
43
43
43
43
43
1.6
ENST00000367103
6
ENSE00001648220
chr1:
206904033-206904108
76
MAPK2_HUMAN
231-256
26
12
A:231-256 (gaps)
B:231-256 (gaps)
C:231-256 (gaps)
D:231-256 (gaps)
E:231-256 (gaps)
F:231-256 (gaps)
G:231-256 (gaps)
H:231-256 (gaps)
I:231-256 (gaps)
J:231-256 (gaps)
K:231-256 (gaps)
L:231-256 (gaps)
26
26
26
26
26
26
26
26
26
26
26
26
1.7
ENST00000367103
7
ENSE00001069544
chr1:
206904483-206904607
125
MAPK2_HUMAN
256-298
43
12
A:256-298 (gaps)
B:256-298 (gaps)
C:256-298 (gaps)
D:256-298 (gaps)
E:256-298 (gaps)
F:256-298 (gaps)
G:256-298 (gaps)
H:256-298 (gaps)
I:256-298 (gaps)
J:256-298 (gaps)
K:256-298 (gaps)
L:256-298 (gaps)
43
43
43
43
43
43
43
43
43
43
43
43
1.8b
ENST00000367103
8b
ENSE00001069550
chr1:
206904985-206905070
86
MAPK2_HUMAN
298-326
29
12
A:298-326
B:298-326
C:298-326
D:298-326
E:298-326
F:298-326
G:298-326
H:298-326
I:298-326
J:298-326
K:298-326
L:298-326
29
29
29
29
29
29
29
29
29
29
29
29
1.9b
ENST00000367103
9b
ENSE00001069552
chr1:
206905184-206905264
81
MAPK2_HUMAN
327-353
27
12
A:327-345
B:327-345
C:327-345
D:327-345
E:327-345
F:327-345
G:327-345
H:327-345
I:327-345
J:327-345
K:327-345
L:327-345
19
19
19
19
19
19
19
19
19
19
19
19
1.9d
ENST00000367103
9d
ENSE00001443498
chr1:
206905920-206907628
1709
MAPK2_HUMAN
354-400
47
0
-
-
[
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]
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d3r2ba_ (A:)
1b: SCOP_d3r2bb_ (B:)
1c: SCOP_d3r2bc_ (C:)
1d: SCOP_d3r2bd_ (D:)
1e: SCOP_d3r2be_ (E:)
1f: SCOP_d3r2bf_ (F:)
1g: SCOP_d3r2bg_ (G:)
1h: SCOP_d3r2bh_ (H:)
1i: SCOP_d3r2bi_ (I:)
1j: SCOP_d3r2bj_ (J:)
1k: SCOP_d3r2bk_ (K:)
1l: SCOP_d3r2bl_ (L:)
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(
)
(
)
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
:
MAP kinase activated protein kinase 2, mapkap2
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d3r2ba_
A:
1b
d3r2bb_
B:
1c
d3r2bc_
C:
1d
d3r2bd_
D:
1e
d3r2be_
E:
1f
d3r2bf_
F:
1g
d3r2bg_
G:
1h
d3r2bh_
H:
1i
d3r2bi_
I:
1j
d3r2bj_
J:
1k
d3r2bk_
K:
1l
d3r2bl_
L:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Select:
Label:
Sorry, no Info available
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Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Pkinase_3r2bL01 (L:64-325)
1b: PFAM_Pkinase_3r2bL02 (L:64-325)
1c: PFAM_Pkinase_3r2bL03 (L:64-325)
1d: PFAM_Pkinase_3r2bL04 (L:64-325)
1e: PFAM_Pkinase_3r2bL05 (L:64-325)
1f: PFAM_Pkinase_3r2bL06 (L:64-325)
1g: PFAM_Pkinase_3r2bL07 (L:64-325)
1h: PFAM_Pkinase_3r2bL08 (L:64-325)
1i: PFAM_Pkinase_3r2bL09 (L:64-325)
1j: PFAM_Pkinase_3r2bL10 (L:64-325)
1k: PFAM_Pkinase_3r2bL11 (L:64-325)
1l: PFAM_Pkinase_3r2bL12 (L:64-325)
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Clans
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(
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Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
1a
Pkinase-3r2bL01
L:64-325
1b
Pkinase-3r2bL02
L:64-325
1c
Pkinase-3r2bL03
L:64-325
1d
Pkinase-3r2bL04
L:64-325
1e
Pkinase-3r2bL05
L:64-325
1f
Pkinase-3r2bL06
L:64-325
1g
Pkinase-3r2bL07
L:64-325
1h
Pkinase-3r2bL08
L:64-325
1i
Pkinase-3r2bL09
L:64-325
1j
Pkinase-3r2bL10
L:64-325
1k
Pkinase-3r2bL11
L:64-325
1l
Pkinase-3r2bL12
L:64-325
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