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4BDI
Asym. Unit
Info
Asym.Unit (104 KB)
Biol.Unit 1 (194 KB)
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(1)
Title
:
FRAGMENT-BASED SCREENING IDENTIFIES A NEW AREA FOR INHIBITOR BINDING TO CHECKPOINT KINASE 2 (CHK2)
Authors
:
M. C. Silva-Santisteban, I. M. Westwood, K. Boxall, N. Brown, S. Peacoc C. Mcandrew, E. Barrie, M. Richards, A. Mirza, A. W. Oliver, R. Burke, S K. Jones, G. W. Aherne, J. Blagg, I. Collins, M. D. Garrett, R. L. M. Van
Date
:
05 Oct 12 (Deposition) - 26 Jun 13 (Release) - 26 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.32
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. C. Silva-Santisteban, I. M. Westwood, K. Boxall, N. Brown, S. Peacock, C. Mcandrew, E. Barrie, M. Richards, A. Mirza, A. W. Oliver R. Burke, S. Hoelder, K. Jones, G. W. Aherne, J. Blagg, I. Collins, M. D. Garrett, R. L. M. Van Montfort
Fragment-Based Screening Maps Inhibitor Interactions In The Atp-Binding Site Of Checkpoint Kinase 2.
Plos One V. 8 65689 2013
[
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]
Hetero Components
(4, 10)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: 1,2-ETHANEDIOL (EDOa)
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)
3a: 1-ACETYL-N-(5-METHYLPYRIDIN-2-YL)P... (HAUa)
4a: NITRATE ION (NO3a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
3
HAU
1
Ligand/Ion
1-ACETYL-N-(5-METHYLPYRIDIN-2-YL)PIPERIDINE-4-CARBOXAMIDE
4
NO3
1
Ligand/Ion
NITRATE ION
[
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]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:226 , VAL A:234 , ALA A:247 , LEU A:301 , GLU A:302 , MET A:304 , GLU A:305 , LEU A:354
BINDING SITE FOR RESIDUE HAU A1516
02
AC2
SOFTWARE
LEU A:375 , GLY A:403 , TYR A:404 , ASN A:405 , ARG A:406
BINDING SITE FOR RESIDUE NO3 A1517
03
AC3
SOFTWARE
TYR A:212 , ARG A:406 , EDO A:1524 , HOH A:2053
BINDING SITE FOR RESIDUE CL A1518
04
AC4
SOFTWARE
ALA A:453 , GLU A:454 , SER A:456
BINDING SITE FOR RESIDUE EDO A1519
05
AC5
SOFTWARE
LYS A:465 , PHE A:475 , GLU A:479 , ARG A:482 , HIS A:483 , PRO A:484 , HOH A:2050
BINDING SITE FOR RESIDUE EDO A1520
06
AC6
SOFTWARE
GLU A:394 , VAL A:395 , HOH A:2032 , HOH A:2052
BINDING SITE FOR RESIDUE EDO A1521
07
AC7
SOFTWARE
LEU A:277 , LYS A:278 , LEU A:280 , LYS A:287 , ILE A:288
BINDING SITE FOR RESIDUE EDO A1522
08
AC8
SOFTWARE
MET A:209 , GLU A:340
BINDING SITE FOR RESIDUE EDO A1523
09
AC9
SOFTWARE
MET A:209 , SER A:210 , TYR A:212 , CL A:1518 , EDO A:1525 , HOH A:2053
BINDING SITE FOR RESIDUE EDO A1524
10
BC1
SOFTWARE
MET A:209 , GLU A:340 , EDO A:1524
BINDING SITE FOR RESIDUE EDO A1525
[
close Site info
]
SAPs(SNPs)/Variants
(18, 18)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_019106 (E239K, chain A, )
02: VAR_019111 (I251F, chain A, )
03: VAR_019112 (R318H, chain A, )
04: VAR_019113 (T323P, chain A, )
05: VAR_019114 (Y327C, chain A, )
06: VAR_029154 (D347N, chain A, )
07: VAR_066012 (H371Y, chain A, )
08: VAR_073020 (Y390C, chain A, )
09: VAR_024572 (R406H, chain A, )
10: VAR_022463 (S428F, chain A, )
11: VAR_021117 (L436M, chain A, )
12: VAR_021118 (N446K, chain A, )
13: VAR_021119 (F447I, chain A, )
14: VAR_021120 (I448S, chain A, )
15: VAR_019115 (T476K, chain A, )
16: VAR_029155 (S500C, chain A, )
17: VAR_021121 (E501K, chain A, )
18: VAR_021122 (L512V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_019106
E
239
K
CHK2_HUMAN
Disease (PC)
---
A
E
239
K
02
UniProt
VAR_019111
I
251
F
CHK2_HUMAN
Disease (PC)
---
A
I
251
F
03
UniProt
VAR_019112
R
318
H
CHK2_HUMAN
Disease (PC)
143611747
A
R
318
H
04
UniProt
VAR_019113
T
323
P
CHK2_HUMAN
Disease (PC)
---
A
T
323
P
05
UniProt
VAR_019114
Y
327
C
CHK2_HUMAN
Disease (PC)
---
A
Y
327
C
06
UniProt
VAR_029154
D
347
N
CHK2_HUMAN
Polymorphism
28909980
A
D
347
N
07
UniProt
VAR_066012
H
371
Y
CHK2_HUMAN
Unclassified
---
A
H
371
Y
08
UniProt
VAR_073020
Y
390
C
CHK2_HUMAN
Disease (BC)
---
A
Y
390
C
09
UniProt
VAR_024572
R
406
H
CHK2_HUMAN
Polymorphism
299671
A
R
406
H
10
UniProt
VAR_022463
S
428
F
CHK2_HUMAN
Polymorphism
137853011
A
S
428
F
11
UniProt
VAR_021117
L
436
M
CHK2_HUMAN
Polymorphism
17882922
A
L
436
M
12
UniProt
VAR_021118
N
446
K
CHK2_HUMAN
Polymorphism
17880867
A
N
446
K
13
UniProt
VAR_021119
F
447
I
CHK2_HUMAN
Polymorphism
17881473
A
F
447
I
14
UniProt
VAR_021120
I
448
S
CHK2_HUMAN
Polymorphism
17886163
A
I
448
S
15
UniProt
VAR_019115
T
476
K
CHK2_HUMAN
Disease (PC)
---
A
T
476
K
16
UniProt
VAR_029155
S
500
C
CHK2_HUMAN
Polymorphism
28909981
A
S
500
C
17
UniProt
VAR_021121
E
501
K
CHK2_HUMAN
Polymorphism
17883172
A
E
501
K
18
UniProt
VAR_021122
L
512
V
CHK2_HUMAN
Polymorphism
17882942
A
L
512
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ST (A:343-355)
;
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.
CHK2_HUMAN
343-355
1
A:343-355
[
close PROSITE info
]
Exons
(11, 11)
Info
All Exons
Exon 1.13 (A:209-227)
Exon 1.14c (A:232-253)
Exon 1.15 (A:267-282)
Exon 1.16 (A:283-303)
Exon 1.17a (A:303-336)
Exon 1.18d (A:337-365)
Exon 1.19a (A:366-420)
Exon 1.20a (A:420-459)
Exon 1.21 (A:459-487)
Exon 1.22c (A:488-514)
Exon 1.23g (A:515-515)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.10c/1.13
02: Boundary 1.13/1.14c
03: Boundary 1.14c/1.15
04: Boundary 1.15/1.16
05: Boundary 1.16/1.17a
06: Boundary 1.17a/1.18d
07: Boundary 1.18d/1.19a
08: Boundary 1.19a/1.20a
09: Boundary 1.20a/1.21
10: Boundary 1.21/1.22c
11: Boundary 1.22c/1.23g
12: Boundary 1.23g/-
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
ENST00000328354
1b
ENSE00001936528
chr22:
29137832-29137757
76
CHK2_HUMAN
-
0
0
-
-
1.4a
ENST00000328354
4a
ENSE00001731305
chr22:
29130715-29130391
325
CHK2_HUMAN
1-107
107
0
-
-
1.9a
ENST00000328354
9a
ENSE00001674473
chr22:
29121355-29121231
125
CHK2_HUMAN
107-148
42
0
-
-
1.10c
ENST00000328354
10c
ENSE00001294552
chr22:
29121112-29120965
148
CHK2_HUMAN
149-198
50
0
-
-
1.13
ENST00000328354
13
ENSE00001778344
chr22:
29115473-29115383
91
CHK2_HUMAN
198-228
31
1
A:209-227
19
1.14c
ENST00000328354
14c
ENSE00002163490
chr22:
29108005-29107897
109
CHK2_HUMAN
228-264
37
1
A:232-253
22
1.15
ENST00000328354
15
ENSE00001690884
chr22:
29106047-29105994
54
CHK2_HUMAN
265-282
18
1
A:267-282
16
1.16
ENST00000328354
16
ENSE00001600063
chr22:
29099554-29099493
62
CHK2_HUMAN
283-303
21
1
A:283-303
21
1.17a
ENST00000328354
17a
ENSE00001751254
chr22:
29095925-29095826
100
CHK2_HUMAN
303-336
34
1
A:303-336
34
1.18d
ENST00000328354
18d
ENSE00001742823
chr22:
29092975-29092889
87
CHK2_HUMAN
337-365
29
1
A:337-365
29
1.19a
ENST00000328354
19a
ENSE00001610753
chr22:
29091861-29091698
164
CHK2_HUMAN
366-420
55
1
A:366-420
55
1.20a
ENST00000328354
20a
ENSE00001744921
chr22:
29091230-29091115
116
CHK2_HUMAN
420-459
40
1
A:420-459
40
1.21
ENST00000328354
21
ENSE00001669857
chr22:
29090105-29090020
86
CHK2_HUMAN
459-487
29
1
A:459-487
29
1.22c
ENST00000328354
22c
ENSE00001622783
chr22:
29085203-29085123
81
CHK2_HUMAN
488-514
27
1
A:488-514
27
1.23g
ENST00000328354
23g
ENSE00001550146
chr22:
29083974-29083732
243
CHK2_HUMAN
515-543
29
1
A:515-515
1
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d4bdia_ (A:)
View:
Select:
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
:
automated matches
(529)
Protein domain
:
automated matches
(529)
Human (Homo sapiens) [TaxId: 9606]
(438)
1a
d4bdia_
A:
[
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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
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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Asym.Unit (104 KB)
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