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.
2VWW
Asym. Unit
Info
Asym.Unit (49 KB)
Biol.Unit 1 (44 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
EPHB4 KINASE DOMAIN INHIBITOR COMPLEX
Authors
:
J. Read, C. A. Brassington, I. Green, E. J. Mccall, A. L. Valentine, D. Ba A. G. Leach, J. G. Kettle
Date
:
27 Jun 08 (Deposition) - 08 Jul 08 (Release) - 28 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Tyrosine-Protein Kinase, Receptor Tyrosine Kinase, Kinase, Mutant, Membrane, Receptor, Transferase, Atp-Binding, Polymorphism, Glycoprotein, Transmembrane, Phosphoprotein, Unphosphorylated, Nucleotide-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Bardelle, D. Cross, S. Davenport, J. G. Kettle, E. J. Ko, A. G. Leach, A. Mortlock, J. Read, N. J. Roberts, P. Robins, E. J. Williams
Inhibitors Of The Tyrosine Kinase Ephb4. Part 1: Structure-Based Design And Optimization Of A Series Of 2, 4-Bis-Anilinopyrimidines
Bioorg. Med. Chem. Lett. V. 18 2776 2008
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: N'-(5-CHLORO-1,3-BENZODIOXOL-4-YL)... (7X2a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
7X2
1
Ligand/Ion
N'-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-N-(3,4,5-TRIMETHOXYPHENYL)PYRIMIDINE-2,4-DIAMINE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:621 , ALA A:645 , LYS A:647 , GLU A:664 , ILE A:677 , ILE A:691 , THR A:693 , GLU A:694 , PHE A:695 , MET A:696 , GLU A:697 , GLY A:699 , ALA A:700 , LEU A:747 , SER A:757 , HOH A:2031 , HOH A:2070 , HOH A:2122
BINDING SITE FOR RESIDUE 7X2 A1888
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_042186 (R678H, chain A, )
2: VAR_042187 (A882T, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_042186
R
678
H
EPHB4_HUMAN
Polymorphism
55692440
A
R
678
H
2
UniProt
VAR_042187
A
882
T
EPHB4_HUMAN
Polymorphism
34918225
A
A
882
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:621-647)
2: PROTEIN_KINASE_TYR (A:736-748)
;
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.
EPHB4_HUMAN
621-647
1
A:621-647
2
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
EPHB4_HUMAN
736-748
1
A:736-748
[
close PROSITE info
]
Exons
(5, 5)
Info
All Exons
Exon 1.11b (A:609-624)
Exon 1.12 (A:624-706 (gaps))
Exon 1.13a (A:707-759)
Exon 1.14a (A:782-828)
Exon 1.15 (A:829-887)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.10/1.11b
2: Boundary 1.11b/1.12
3: Boundary 1.12/1.13a
4: Boundary 1.13a/1.14a
5: Boundary 1.14a/1.15
6: Boundary 1.15/1.16
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
ENST00000358173
1b
ENSE00001868923
chr7:
100425121-100424601
521
EPHB4_HUMAN
1-18
18
0
-
-
1.2b
ENST00000358173
2b
ENSE00000825052
chr7:
100421895-100421825
71
EPHB4_HUMAN
18-41
24
0
-
-
1.3
ENST00000358173
3
ENSE00000825051
chr7:
100421553-100421266
288
EPHB4_HUMAN
42-137
96
0
-
-
1.4
ENST00000358173
4
ENSE00000825050
chr7:
100420289-100419893
397
EPHB4_HUMAN
138-270
133
0
-
-
1.5b
ENST00000358173
5b
ENSE00000825049
chr7:
100417918-100417763
156
EPHB4_HUMAN
270-322
53
0
-
-
1.6
ENST00000358173
6
ENSE00000825048
chr7:
100417511-100417179
333
EPHB4_HUMAN
322-433
112
0
-
-
1.7b
ENST00000358173
7b
ENSE00000710240
chr7:
100416266-100416142
125
EPHB4_HUMAN
433-474
42
0
-
-
1.8c
ENST00000358173
8c
ENSE00001706820
chr7:
100414979-100414814
166
EPHB4_HUMAN
475-530
56
0
-
-
1.9c
ENST00000358173
9c
ENSE00001665919
chr7:
100411643-100411541
103
EPHB4_HUMAN
530-564
35
0
-
-
1.10
ENST00000358173
10
ENSE00001787983
chr7:
100411338-100411274
65
EPHB4_HUMAN
564-586
23
0
-
-
1.11b
ENST00000358173
11b
ENSE00001754468
chr7:
100410830-100410717
114
EPHB4_HUMAN
586-624
39
1
A:609-624
16
1.12
ENST00000358173
12
ENSE00001631272
chr7:
100410616-100410369
248
EPHB4_HUMAN
624-706
83
1
A:624-706 (gaps)
83
1.13a
ENST00000358173
13a
ENSE00001753966
chr7:
100405202-100404987
216
EPHB4_HUMAN
707-778
72
1
A:707-759
53
1.14a
ENST00000358173
14a
ENSE00001623534
chr7:
100404191-100404042
150
EPHB4_HUMAN
779-828
50
1
A:782-828
47
1.15
ENST00000358173
15
ENSE00001783205
chr7:
100403316-100403123
194
EPHB4_HUMAN
829-893
65
1
A:829-887
59
1.16
ENST00000358173
16
ENSE00001649970
chr7:
100402943-100402788
156
EPHB4_HUMAN
893-945
53
0
-
-
1.17b
ENST00000358173
17b
ENSE00001639386
chr7:
100401212-100400187
1026
EPHB4_HUMAN
945-987
43
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2vwwa_ (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
d2vwwa_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2vwwA01 (A:609-695)
2a: CATH_2vwwA02 (A:696-884)
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
2vwwA01
A:609-695
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
2a
2vwwA02
A:696-884
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Pkinase_Tyr_2vwwA01 (A:615-874)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase_Tyr
(229)
Homo sapiens (Human)
(202)
1a
Pkinase_Tyr-2vwwA01
A:615-874
[
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
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 (49 KB)
Header - Asym.Unit
Biol.Unit 1 (44 KB)
Header - Biol.Unit 1
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
2VWW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
