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1YWN
Asym. Unit
Info
Asym.Unit (57 KB)
Biol.Unit 1 (52 KB)
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(1)
Title
:
VEGFR2 IN COMPLEX WITH A NOVEL 4-AMINO-FURO[2,3-D]PYRIMIDINE
Authors
:
Y. Miyazaki, S. Matsunaga, J. Tang, Y. Maeda, M. Nakano, R. J. Philippe, M. Shibahara, W. Liu, H. Sato, L. Wang, R. T. Nolte
Date
:
18 Feb 05 (Deposition) - 23 Aug 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.71
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Miyazaki, S. Matsunaga, J. Tang, Y. Maeda, M. Nakano, R. J. Philippe M. Shibahara, W. Liu, H. Sato, L. Wang, R. T. Nolte
Novel 4-Amino-Furo[2, 3-D]Pyrimidines As Tie-2 And Vegfr2 Dual Inhibitors
Bioorg. Med. Chem. Lett. V. 15 2203 2005
(for further references see the
PDB file header
)
[
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]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: N-{4-[4-AMINO-6-(4-METHOXYPHENYL)F... (LIFa)
2a: O-PHOSPHOTYROSINE (PTRa)
2b: O-PHOSPHOTYROSINE (PTRb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LIF
1
Ligand/Ion
N-{4-[4-AMINO-6-(4-METHOXYPHENYL)FURO[2,3-D]PYRIMIDIN-5-YL]PHENYL}-N'-[2-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]UREA
2
PTR
2
Mod. Amino Acid
O-PHOSPHOTYROSINE
[
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]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:127 , LEU A:838 , GLY A:839 , ARG A:840 , GLY A:841 , VAL A:846 , ALA A:864 , GLU A:883 , VAL A:896 , VAL A:897 , GLU A:915 , PHE A:916 , CYS A:917 , LEU A:1017 , HIS A:1024 , ILE A:1042 , CYS A:1043 , ASP A:1044
BINDING SITE FOR RESIDUE LIF A 301
[
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]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_046679 (V846E, chain A, )
2: VAR_042061 (A1063T, chain A, )
3: VAR_063147 (P1145S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_046679
V
848
E
VGFR2_HUMAN
Polymorphism
1139776
A
V
846
E
2
UniProt
VAR_042061
A
1065
T
VGFR2_HUMAN
Polymorphism
56302315
A
A
1063
T
3
UniProt
VAR_063147
P
1147
S
VGFR2_HUMAN
Disease (HCI)
---
A
P
1145
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:838-866)
2: RECEPTOR_TYR_KIN_III (A:891-904)
3: PROTEIN_KINASE_TYR (A:1022-1034)
;
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.
VGFR2_HUMAN
840-868
1
A:838-866
2
RECEPTOR_TYR_KIN_III
PS00240
Receptor tyrosine kinase class III signature.
VGFR2_HUMAN
893-906
1
A:891-904
3
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
VGFR2_HUMAN
1024-1036
1
A:1022-1034
[
close PROSITE info
]
Exons
(10, 10)
Info
All Exons
Exon 1.17 (A:818-835)
Exon 1.18 (A:835-868)
Exon 1.19b (A:873-908)
Exon 1.20 (A:908-935)
Exon 1.22 (A:997-1021)
Exon 1.23 (A:1022-1062 (gaps))
Exon 1.24 (A:1063-1100)
Exon 1.25 (A:1100-1133)
Exon 1.26 (A:1133-1168)
Exon 1.27 (A:1169-1169)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.16/1.17
02: Boundary 1.17/1.18
03: Boundary 1.18/1.19b
04: Boundary 1.19b/1.20
05: Boundary 1.20/1.21b
06: Boundary 1.21b/1.22
07: Boundary 1.22/1.23
08: Boundary 1.23/1.24
09: Boundary 1.24/1.25
10: Boundary 1.25/1.26
11: Boundary 1.26/1.27
12: Boundary 1.27/1.28
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
1.1a
ENST00000263923
1a
ENSE00001171700
chr4:
55991756-55991394
363
VGFR2_HUMAN
1-23
23
0
-
-
1.2
ENST00000263923
2
ENSE00000716050
chr4:
55987357-55987264
94
VGFR2_HUMAN
23-54
32
0
-
-
1.3
ENST00000263923
3
ENSE00000716047
chr4:
55984967-55984771
197
VGFR2_HUMAN
54-120
67
0
-
-
1.4
ENST00000263923
4
ENSE00000716045
chr4:
55981578-55981448
131
VGFR2_HUMAN
120-163
44
0
-
-
1.5
ENST00000263923
5
ENSE00000716043
chr4:
55981209-55981041
169
VGFR2_HUMAN
164-220
57
0
-
-
1.6
ENST00000263923
6
ENSE00000716040
chr4:
55980432-55980293
140
VGFR2_HUMAN
220-266
47
0
-
-
1.7
ENST00000263923
7
ENSE00000716038
chr4:
55979648-55979471
178
VGFR2_HUMAN
267-326
60
0
-
-
1.8
ENST00000263923
8
ENSE00000716036
chr4:
55976935-55976821
115
VGFR2_HUMAN
326-364
39
0
-
-
1.9
ENST00000263923
9
ENSE00000580228
chr4:
55976733-55976570
164
VGFR2_HUMAN
364-419
56
0
-
-
1.10
ENST00000263923
10
ENSE00000716032
chr4:
55974060-55973904
157
VGFR2_HUMAN
419-471
53
0
-
-
1.11
ENST00000263923
11
ENSE00000716030
chr4:
55972977-55972854
124
VGFR2_HUMAN
471-512
42
0
-
-
1.12
ENST00000263923
12
ENSE00000716029
chr4:
55972107-55971999
109
VGFR2_HUMAN
513-549
37
0
-
-
1.13a
ENST00000263923
13a
ENSE00001074496
chr4:
55971151-55970810
342
VGFR2_HUMAN
549-663
115
0
-
-
1.14
ENST00000263923
14
ENSE00000716025
chr4:
55968675-55968529
147
VGFR2_HUMAN
663-712
50
0
-
-
1.15
ENST00000263923
15
ENSE00000716023
chr4:
55968195-55968064
132
VGFR2_HUMAN
712-756
45
0
-
-
1.16
ENST00000263923
16
ENSE00000716022
chr4:
55964970-55964864
107
VGFR2_HUMAN
756-791
36
0
-
-
1.17
ENST00000263923
17
ENSE00000716020
chr4:
55964439-55964304
136
VGFR2_HUMAN
792-837
46
1
A:818-835
18
1.18
ENST00000263923
18
ENSE00000716018
chr4:
55963933-55963829
105
VGFR2_HUMAN
837-872
36
1
A:835-868
34
1.19b
ENST00000263923
19b
ENSE00001312000
chr4:
55962509-55962396
114
VGFR2_HUMAN
872-910
39
1
A:873-908
36
1.20
ENST00000263923
20
ENSE00000716016
chr4:
55961832-55961744
89
VGFR2_HUMAN
910-939
30
1
A:908-935
28
1.21b
ENST00000263923
21b
ENSE00000716015
chr4:
55961122-55960969
154
VGFR2_HUMAN
940-991
52
0
-
-
1.22
ENST00000263923
22
ENSE00000877921
chr4:
55958881-55958784
98
VGFR2_HUMAN
991-1023
33
1
A:997-1021
25
1.23
ENST00000263923
23
ENSE00001608690
chr4:
55956245-55956123
123
VGFR2_HUMAN
1024-1064
41
1
A:1022-1062 (gaps)
41
1.24
ENST00000263923
24
ENSE00000877919
chr4:
55955969-55955858
112
VGFR2_HUMAN
1065-1102
38
1
A:1063-1100
38
1.25
ENST00000263923
25
ENSE00000877918
chr4:
55955640-55955541
100
VGFR2_HUMAN
1102-1135
34
1
A:1100-1133
34
1.26
ENST00000263923
26
ENSE00000877917
chr4:
55955140-55955035
106
VGFR2_HUMAN
1135-1170
36
1
A:1133-1168
36
1.27
ENST00000263923
27
ENSE00000877916
chr4:
55953925-55953774
152
VGFR2_HUMAN
1171-1221
51
1
A:1169-1169
1
1.28
ENST00000263923
28
ENSE00000877915
chr4:
55948802-55948703
100
VGFR2_HUMAN
1221-1254
34
0
-
-
1.29
ENST00000263923
29
ENSE00001148006
chr4:
55948208-55948123
86
VGFR2_HUMAN
1255-1283
29
0
-
-
1.30
ENST00000263923
30
ENSE00001171693
chr4:
55946330-55944644
1687
VGFR2_HUMAN
1283-1356
74
0
-
-
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1ywna_ (A:)
View:
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Classes
(
)
(
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Folds
(
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(
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(
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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
:
Vascular endothelial growth factor receptor 2 (kdr)
(20)
Human (Homo sapiens) [TaxId: 9606]
(20)
1a
d1ywna_
A:
[
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1ywnA01 (A:818-916)
2a: CATH_1ywnA02 (A:917-1164)
View:
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Classes
(
)
(
)
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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
1ywnA01
A:818-916
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
1ywnA02
A:917-1164
[
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]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Pkinase_Tyr_1ywnA01 (A:832-1158)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase_Tyr
(229)
Homo sapiens (Human)
(202)
1a
Pkinase_Tyr-1ywnA01
A:832-1158
[
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Asymmetric Unit 1
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