PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2WIH
Asym. Unit
Info
Asym.Unit (197 KB)
Biol.Unit 1 (96 KB)
Biol.Unit 2 (96 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF CDK2-CYCLIN A WITH PHA-848125
Authors
:
M. G. Brasca, N. Amboldi, D. Ballinari, A. D. Cameron, E. Casale, G. Cervi, M. Colombo, F. Colotta, V. Croci, R. Dalessio, F. Fiorentini, A. Isacchi, C. Mercurio, W. Moretti, A. Panzeri, W. Pastori, P. Pevarello, F. Quartieri, F. Roletto, G. Traquandi, P. Vianello, A. Vulpetti, M. Ciomei
Date
:
13 May 09 (Deposition) - 28 Jul 09 (Release) - 20 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Cell Cycle, Atp-Binding, Transferase, Polymorphism, Phosphorylation, Nucleotide-Binding, Cell Division, Serine/Threonine-Protein 2 Kinase, Phosphoprotein, Serine/Threonine-Protein Kinase, Mitosis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. G. Brasca, N. Amboldi, D. Ballinari, A. D. Cameron, E. Casale, G. Cervi, M. Colombo, F. Colotta, V. Croci, R. Dalessio, F. Fiorentini, A. Isacchi, C. Mercurio, W. Moretti, A. Panzeri, W. Pastori, P. Pevarello, F. Quartieri, F. Roletto, G. Traquandi, P. Vianello, A. Vulpetti, M. Ciomei
Identification Of N, 1, 4, 4-Tetramethyl-8-{[4-(4- Methylpiperazin-1-Yl)Phenyl]Amino}-4, 5-Dihydro-1H- Pyrazolo[4, 3-H]Quinazoline-3-Carboxamide (Pha- 848125), A Potent, Orally Available Cyclin Dependent Kinase Inhibitor.
J. Med. Chem. V. 52 5152 2009
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: N,1,4,4-TETRAMETHYL-8-{[4-(4-METHY... (P48a)
1b: N,1,4,4-TETRAMETHYL-8-{[4-(4-METHY... (P48b)
2a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
P48
2
Ligand/Ion
N,1,4,4-TETRAMETHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE
2
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG D:410 , LYS D:414 , HOH D:2079
BINDING SITE FOR RESIDUE SO4 D1433
2
AC2
SOFTWARE
TYR C:15 , ALA C:31 , LYS C:33 , PHE C:80 , GLU C:81 , LEU C:83 , HIS C:84 , GLN C:85 , ASP C:86 , LYS C:89 , LEU C:134 , ASP C:145
BINDING SITE FOR RESIDUE P48 C1299
3
AC3
SOFTWARE
VAL A:18 , ALA A:31 , LYS A:33 , PHE A:80 , GLU A:81 , LEU A:83 , HIS A:84 , GLN A:85 , LEU A:134 , ASP A:145
BINDING SITE FOR RESIDUE P48 A1299
[
close Site info
]
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)
[
close SNP/Variant info
]
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:
Select:
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
[
close PROSITE info
]
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:265-298 | C:265-298)
Exon 2.3 (B:176-190 | D:176-190)
Exon 2.4 (B:191-265 | D:191-265)
Exon 2.5 (B:265-334 | D:265-334 (gaps))
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:
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
1.1
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:265-298
C:265-298
34
34
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:176-190
D:176-190
15
15
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 (gaps)
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_d2wihb1 (B:176-309)
1b: SCOP_d2wihb2 (B:310-432)
1c: SCOP_d2wihd1 (D:176-309)
1d: SCOP_d2wihd2 (D:310-432)
2a: SCOP_d2wiha_ (A:)
2b: SCOP_d2wihc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d2wihb1
B:176-309
1b
d2wihb2
B:310-432
1c
d2wihd1
D:176-309
1d
d2wihd2
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
:
automated matches
(542)
Human (Homo sapiens) [TaxId: 9606]
(452)
2a
d2wiha_
A:
2b
d2wihc_
C:
[
close SCOP info
]
CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_2wihA01 (A:1-84)
1b: CATH_2wihC01 (C:1-84)
2a: CATH_2wihD01 (D:181-194,D:308-432)
2b: CATH_2wihB02 (B:195-307)
2c: CATH_2wihD02 (D:195-307)
2d: CATH_2wihB01 (B:181-194,B:308-432)
3a: CATH_2wihA02 (A:85-297)
3b: CATH_2wihC02 (C:85-297)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
2wihA01
A:1-84
1b
2wihC01
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
2wihD01
D:181-194,D:308-432
2b
2wihB02
B:195-307
2c
2wihD02
D:195-307
2d
2wihB01
B:181-194,B:308-432
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
3a
2wihA02
A:85-297
3b
2wihC02
C:85-297
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Cyclin_C_2wihD01 (D:309-427)
1b: PFAM_Cyclin_C_2wihD02 (D:309-427)
2a: PFAM_Cyclin_N_2wihD03 (D:181-307)
2b: PFAM_Cyclin_N_2wihD04 (D:181-307)
3a: PFAM_Pkinase_2wihC01 (C:4-286)
3b: PFAM_Pkinase_2wihC02 (C:4-286)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cyclin
(63)
Family
:
Cyclin_C
(40)
Homo sapiens (Human)
(36)
1a
Cyclin_C-2wihD01
D:309-427
1b
Cyclin_C-2wihD02
D:309-427
Family
:
Cyclin_N
(51)
Homo sapiens (Human)
(43)
2a
Cyclin_N-2wihD03
D:181-307
2b
Cyclin_N-2wihD04
D:181-307
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
3a
Pkinase-2wihC01
C:4-286
3b
Pkinase-2wihC02
C:4-286
[
close Pfam info
]
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
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (197 KB)
Header - Asym.Unit
Biol.Unit 1 (96 KB)
Header - Biol.Unit 1
Biol.Unit 2 (96 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2WIH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
