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2UUE
Asym. Unit
Info
Asym.Unit (201 KB)
Biol.Unit 1 (98 KB)
Biol.Unit 2 (98 KB)
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(1)
Title
:
REPLACE: A STRATEGY FOR ITERATIVE DESIGN OF CYCLIN BINDING GROOVE INHIBITORS
Authors
:
M. J. Andrews, G. Kontopidis, C. Mcinnes, A. Plater, L. Innes, A. Cowan, P. Jewsbury, P. M. Fischer
Date
:
02 Mar 07 (Deposition) - 27 Mar 07 (Release) - 05 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.06
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,E (1x)
Biol. Unit 2: C,D,F (1x)
Keywords
:
Polymorphism, Cyclin Groove, Cell Division, Cdk2, Kinase, Cyclin, Active, Mitosis, Inhibition, Phosphorylation, Nucleotide-Binding, Serine/Threonine-Protein Kinase, Cell Cycle, Nonpeptide, Transferase, Atp-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Andrews, G. Kontopidis, C. Mcinnes, A. Plater, L. Innes, A. Cowan, P. Jewsbury, P. M. Fischer
Replace: A Strategy For Iterative Design Of Cyclin- Binding Groove Inhibitors
Chembiochem V. 7 1909 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: 1-(3,5-DICHLOROPHENYL)-5-METHYL-1H... (GVCa)
1b: 1-(3,5-DICHLOROPHENYL)-5-METHYL-1H... (GVCb)
2a: 4-METHYL-5-{(2E)-2-[(4-MORPHOLIN-4... (MTZa)
2b: 4-METHYL-5-{(2E)-2-[(4-MORPHOLIN-4... (MTZb)
3a: AMINO GROUP (NH2a)
3b: AMINO GROUP (NH2b)
4a: 4-FLUORO-L-PHENYLALANINE (PFFa)
4b: 4-FLUORO-L-PHENYLALANINE (PFFb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GVC
2
Ligand/Ion
1-(3,5-DICHLOROPHENYL)-5-METHYL-1H-1,2,4-TRIAZOLE-3-CARBOXYLIC ACID
2
MTZ
2
Ligand/Ion
4-METHYL-5-{(2E)-2-[(4-MORPHOLIN-4-YLPHENYL)IMINO]-2,5-DIHYDROPYRIMIDIN-4-YL}-1,3-THIAZOL-2-AMINE
3
NH2
2
Mod. Amino Acid
AMINO GROUP
4
PFF
2
Mod. Amino Acid
4-FLUORO-L-PHENYLALANINE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:10 , ALA A:31 , LYS A:33 , PHE A:80 , GLU A:81 , PHE A:82 , LEU A:83 , HIS A:84 , GLN A:85 , ASP A:86 , LYS A:89 , LEU A:134 , HOH A:2015
BINDING SITE FOR RESIDUE MTZ A1297
2
AC2
SOFTWARE
ILE C:10 , GLU C:12 , ALA C:31 , GLU C:81 , PHE C:82 , LEU C:83 , HIS C:84 , LEU C:134 , HOH C:2012
BINDING SITE FOR RESIDUE MTZ C1298
3
AC3
SOFTWARE
GLU A:12 , TRP B:217 , GLU B:220 , VAL B:221 , GLN B:254 , ILE B:281 , ASP B:283 , ARG E:1 , LEU E:2
BINDING SITE FOR RESIDUE GVC E1433
4
AC4
SOFTWARE
TRP D:217 , GLU D:220 , VAL D:221 , GLN D:254 , ILE D:281 , THR D:282 , ASP D:283 , ARG F:1 , LEU F:2
BINDING SITE FOR RESIDUE GVC F1433
[
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SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016157 (Y15S, chain A/C, )
2: VAR_053927 (V18L, chain A/C, )
3: VAR_041972 (P45L, chain A/C, )
4: VAR_019988 (T290S, chain A/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016157
Y
15
S
CDK2_HUMAN
Polymorphism
3087335
A/C
Y
15
S
2
UniProt
VAR_053927
V
18
L
CDK2_HUMAN
Polymorphism
11554376
A/C
V
18
L
3
UniProt
VAR_041972
P
45
L
CDK2_HUMAN
Unclassified
---
A/C
P
45
L
4
UniProt
VAR_019988
T
290
S
CDK2_HUMAN
Polymorphism
2069413
A/C
T
290
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:10-33,C:10-33)
2: PROTEIN_KINASE_ST (A:123-135,C:123-135)
3: CYCLINS (B:211-242,D:211-242)
;
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.
CDK2_HUMAN
10-33
2
A:10-33
C:10-33
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
CDK2_HUMAN
123-135
2
A:123-135
C:123-135
3
CYCLINS
PS00292
Cyclins signature.
CCNA2_HUMAN
211-242
2
B:211-242
D:211-242
[
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Exons
(13, 26)
Info
All Exons
Exon 1.1 (A:1-39 | C:1-39)
Exon 1.2 (A:39-65 | C:39-65)
Exon 1.3 (A:65-105 | C:65-105)
Exon 1.4 (A:106-162 | C:106-162)
Exon 1.5 (A:163-196 | C:163-196)
Exon 1.6 (A:197-264 | C:197-264)
Exon 1.7 (A:265-296 | C:265-297)
Exon 2.3 (B:175-190 | D:175-190)
Exon 2.4 (B:191-265 | D:191-265)
Exon 2.5 (B:265-334 | D:265-334)
Exon 2.6 (B:335-372 | D:335-372)
Exon 2.7 (B:373-417 | D:373-417)
Exon 2.8 (B:417-432 | D:417-432)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/-
09: Boundary 2.2/2.3
10: Boundary 2.3/2.4
11: Boundary 2.4/2.5
12: Boundary 2.5/2.6
13: Boundary 2.6/2.7
14: Boundary 2.7/2.8
15: Boundary 2.8/-
View:
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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
1.1
ENST00000266970
1
ENSE00001301614
chr12:
56360556-56360908
353
CDK2_HUMAN
1-39
39
2
A:1-39
C:1-39
39
39
1.2
ENST00000266970
2
ENSE00000838625
chr12:
56361641-56361718
78
CDK2_HUMAN
39-65
27
2
A:39-65
C:39-65
27
27
1.3
ENST00000266970
3
ENSE00000838626
chr12:
56361833-56361953
121
CDK2_HUMAN
65-105
41
2
A:65-105
C:65-105
41
41
1.4
ENST00000266970
4
ENSE00000838629
chr12:
56362562-56362732
171
CDK2_HUMAN
106-162
57
2
A:106-162
C:106-162
57
57
1.5
ENST00000266970
5
ENSE00001704611
chr12:
56363259-56363360
102
CDK2_HUMAN
163-196
34
2
A:163-196
C:163-196
34
34
1.6
ENST00000266970
6
ENSE00000938649
chr12:
56364828-56365031
204
CDK2_HUMAN
197-264
68
2
A:197-264
C:197-264
68
68
1.7
ENST00000266970
7
ENSE00001215687
chr12:
56365305-56366565
1261
CDK2_HUMAN
265-298
34
2
A:265-296
C:265-297
32
33
2.1
ENST00000274026
1
ENSE00001176937
chr4:
122745087-122744571
517
CCNA2_HUMAN
1-71
71
0
-
-
2.2
ENST00000274026
2
ENSE00000970332
chr4:
122743801-122743558
244
CCNA2_HUMAN
72-153
82
0
-
-
2.3
ENST00000274026
3
ENSE00000970333
chr4:
122742246-122742134
113
CCNA2_HUMAN
153-190
38
2
B:175-190
D:175-190
16
16
2.4
ENST00000274026
4
ENSE00000970329
chr4:
122741920-122741697
224
CCNA2_HUMAN
191-265
75
2
B:191-265
D:191-265
75
75
2.5
ENST00000274026
5
ENSE00000970330
chr4:
122740734-122740527
208
CCNA2_HUMAN
265-334
70
2
B:265-334
D:265-334
70
70
2.6
ENST00000274026
6
ENSE00001016934
chr4:
122740068-122739955
114
CCNA2_HUMAN
335-372
38
2
B:335-372
D:335-372
38
38
2.7
ENST00000274026
7
ENSE00001016935
chr4:
122739332-122739199
134
CCNA2_HUMAN
373-417
45
2
B:373-417
D:373-417
45
45
2.8
ENST00000274026
8
ENSE00001176933
chr4:
122738841-122737599
1243
CCNA2_HUMAN
417-432
16
2
B:417-432
D:417-432
16
16
[
close EXON info
]
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d2uueb1 (B:175-309)
1b: SCOP_d2uueb2 (B:310-432)
1c: SCOP_d2uued1 (D:175-309)
1d: SCOP_d2uued2 (D:310-432)
2a: SCOP_d2uuea_ (A:)
2b: SCOP_d2uuec_ (C:)
View:
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(
)
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)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cyclin-like
(137)
Superfamily
:
Cyclin-like
(137)
Family
:
Cyclin
(117)
Protein domain
:
Cyclin A
(82)
Human (Homo sapiens) [TaxId: 9606]
(73)
1a
d2uueb1
B:175-309
1b
d2uueb2
B:310-432
1c
d2uued1
D:175-309
1d
d2uued2
D:310-432
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
:
Cyclin-dependent PK, CDK2
(340)
Human (Homo sapiens) [TaxId: 9606]
(336)
2a
d2uuea_
A:
2b
d2uuec_
C:
[
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CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_2uueA01 (A:1-84)
1b: CATH_2uueC01 (C:1-84)
2a: CATH_2uueB01 (B:181-194,B:308-432)
2b: CATH_2uueD01 (D:181-194,D:308-432)
2c: CATH_2uueB02 (B:195-307)
2d: CATH_2uueD02 (D:195-307)
3a: CATH_2uueA02 (A:85-296)
3b: CATH_2uueC02 (C:85-297)
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)
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)
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Phosphorylase Kinase; domain 1
(1392)
Homologous Superfamily
:
Phosphorylase Kinase; domain 1
(1392)
Human (Homo sapiens)
(1036)
1a
2uueA01
A:1-84
1b
2uueC01
C:1-84
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cyclin A; domain 1
(136)
Homologous Superfamily
:
[code=1.10.472.10, no name defined]
(99)
Human (Homo sapiens)
(84)
2a
2uueB01
B:181-194,B:308-432
2b
2uueD01
D:181-194,D:308-432
2c
2uueB02
B:195-307
2d
2uueD02
D:195-307
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
3a
2uueA02
A:85-296
3b
2uueC02
C:85-297
[
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]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Cyclin_C_2uueD01 (D:309-427)
1b: PFAM_Cyclin_C_2uueD02 (D:309-427)
2a: PFAM_Cyclin_N_2uueD03 (D:181-307)
2b: PFAM_Cyclin_N_2uueD04 (D:181-307)
3a: PFAM_Pkinase_2uueC01 (C:4-286)
3b: PFAM_Pkinase_2uueC02 (C:4-286)
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Clans
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cyclin
(63)
Family
:
Cyclin_C
(40)
Homo sapiens (Human)
(36)
1a
Cyclin_C-2uueD01
D:309-427
1b
Cyclin_C-2uueD02
D:309-427
Family
:
Cyclin_N
(51)
Homo sapiens (Human)
(43)
2a
Cyclin_N-2uueD03
D:181-307
2b
Cyclin_N-2uueD04
D:181-307
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
3a
Pkinase-2uueC01
C:4-286
3b
Pkinase-2uueC02
C:4-286
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Asym.Unit (201 KB)
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