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4DSN
Asym. Unit
Info
Asym.Unit (71 KB)
Biol.Unit 1 (66 KB)
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(1)
Title
:
SMALL-MOLECULE LIGANDS BIND TO A DISTINCT POCKET IN RAS AND INHIBIT SOS-MEDIATED NUCLEOTIDE EXCHANGE ACTIVITY
Authors
:
A. Oh, T. Maurer, L. S. Garrenton, K. Pitts, D. J. Anderson, N. J. Skelton B. P. Fauber, B. Pan, S. Malek, D. Stokoe, M. Ludlam, K. K. Bowman, J. Wu, A. M. Giannetti, M. A. Starovasnik, I. Mellman, P. K. Jackson, J. Ruldo G. Fang, W. Wang
Date
:
19 Feb 12 (Deposition) - 25 Apr 12 (Release) - 06 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.03
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Small G-Protein, Signaling, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Maurer, L. S. Garrenton, A. Oh, K. Pitts, D. J. Anderson, N. J. Skelton, B. P. Fauber, B. Pan, S. Malek, D. Stokoe, M. J. Ludlam, K. K. Bowman, J. Wu, A. M. Giannetti, M. A. Starovasnik, I. Mellman, P. K. Jackson, J. Rudolph, W. Wang, G. Fang
Small-Molecule Ligands Bind To A Distinct Pocket In Ras And Inhibit Sos-Mediated Nucleotide Exchange Activity.
Proc. Natl. Acad. Sci. Usa V. 109 5299 2012
[
close entry info
]
Hetero Components
(3, 5)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
2a: PHOSPHOMETHYLPHOSPHONIC ACID GUANY... (GCPa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
2
GCP
1
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
3
MG
2
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:12 , GLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , VAL A:29 , ASP A:30 , GLU A:31 , TYR A:32 , PRO A:34 , THR A:35 , GLY A:60 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , MG A:202 , HOH A:301 , HOH A:302 , HOH A:303 , HOH A:309 , HOH A:319 , HOH A:333 , HOH A:336
BINDING SITE FOR RESIDUE GCP A 201
2
AC2
SOFTWARE
SER A:17 , THR A:35 , GCP A:201 , HOH A:301 , HOH A:302
BINDING SITE FOR RESIDUE MG A 202
3
AC3
SOFTWARE
GLY A:10 , ALA A:59 , GLY A:60 , TYR A:96 , HOH A:305 , HOH A:365
BINDING SITE FOR RESIDUE MG A 203
4
AC4
SOFTWARE
LYS A:101 , ASP A:105 , SER A:106 , GLU A:107
BINDING SITE FOR RESIDUE EDO A 204
5
AC5
SOFTWARE
THR A:35 , ILE A:36 , GLU A:37 , ASP A:38 , THR A:148
BINDING SITE FOR RESIDUE EDO A 205
[
close Site info
]
SAPs(SNPs)/Variants
(43, 43)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_065144 (K5E, chain A, )
02: VAR_064849 (K5N, chain A, )
03: VAR_036305 (D12A, chain A, )
04: VAR_RASK_HUMAN_CCDS8702_1_07 (D12A, chain A, )
05: VAR_006839 (D12C, chain A, )
06: VAR_016026 (D12D, chain A, )
07: VAR_RASK_HUMAN_CCDS8702_1_02 (D12D, chain A, )
08: VAR_RASK_HUMAN_CCDS8702_1_03 (D12D, chain A, )
09: VAR_RASK_HUMAN_CCDS8702_1_08 (D12D, chain A, )
10: VAR_RASK_HUMAN_CCDS8702_1_09 (D12D, chain A, )
11: VAR_016027 (D12R, chain A, )
12: VAR_016028 (D12S, chain A, )
13: VAR_RASK_HUMAN_CCDS8702_1_01 (D12S, chain A, )
14: VAR_006840 (D12V, chain A, )
15: VAR_RASK_HUMAN_CCDS8702_1_04 (D12V, chain A, )
16: VAR_RASK_HUMAN_CCDS8702_1_05 (D12V, chain A, )
17: VAR_RASK_HUMAN_CCDS8702_1_06 (D12V, chain A, )
18: VAR_016029 (G13D, chain A, )
19: VAR_RASK_HUMAN_CCDS8702_1_10 (G13D, chain A, )
20: VAR_RASK_HUMAN_CCDS8702_1_11 (G13D, chain A, )
21: VAR_RASK_HUMAN_CCDS8702_1_12 (G13D, chain A, )
22: VAR_065145 (G13R, chain A, )
23: VAR_026109 (V14I, chain A, )
24: VAR_064850 (Q22E, chain A, )
25: VAR_064851 (Q22R, chain A, )
26: VAR_064852 (P34L, chain A, )
27: VAR_064853 (P34Q, chain A, )
28: VAR_026110 (P34R, chain A, )
29: VAR_064854 (I36M, chain A, )
30: VAR_026111 (T58I, chain A, )
31: VAR_016030 (A59T, chain A, )
32: VAR_026112 (G60R, chain A, )
33: VAR_065146 (G60S, chain A, )
34: VAR_006841 (Q61H, chain A, )
35: VAR_036306 (Q61R, chain A, )
36: VAR_RASK_HUMAN_CCDS8702_1_13 (Q61R, chain A, )
37: VAR_069784 (Y71H, chain A, )
38: VAR_036307 (K117N, chain A, )
39: VAR_RASK_HUMAN_CCDS8702_1_14 (K117N, chain A, )
40: VAR_036308 (A146T, chain A, )
41: VAR_RASK_HUMAN_CCDS8702_1_15 (A146T, chain A, )
42: VAR_RASK_HUMAN_CCDS8702_1_16 (A146T, chain A, )
43: VAR_069785 (K147E, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_065144
K
5
E
RASK_HUMAN
Disease (NS3)
---
A
K
5
E
02
UniProt
VAR_064849
K
5
N
RASK_HUMAN
Disease (GASC)
---
A
K
5
N
03
UniProt
VAR_036305
G
12
A
RASK_HUMAN
Unclassified
---
A
D
12
A
04
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_07
*
G
12
A
RASK_HUMAN
Disease (Colorectal cancer)
---
A
D
12
A
05
UniProt
VAR_006839
G
12
C
RASK_HUMAN
Unclassified
---
A
D
12
C
06
UniProt
VAR_016026
G
12
D
RASK_HUMAN
Unclassified
---
A
D
12
D
07
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_02
*
G
12
D
RASK_HUMAN
Disease (Colorectal cancer)
---
A
D
12
D
08
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_03
*
G
12
D
RASK_HUMAN
Disease (Colorectal cancer)
---
A
D
12
D
09
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_08
*
G
12
D
RASK_HUMAN
Disease (Colorectal cancer)
---
A
D
12
D
10
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_09
*
G
12
D
RASK_HUMAN
Disease (Colorectal cancer)
---
A
D
12
D
11
UniProt
VAR_016027
G
12
R
RASK_HUMAN
Unclassified
---
A
D
12
R
12
UniProt
VAR_016028
G
12
S
RASK_HUMAN
Unclassified
---
A
D
12
S
13
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_01
*
G
12
S
RASK_HUMAN
Disease (Colorectal cancer)
---
A
D
12
S
14
UniProt
VAR_006840
G
12
V
RASK_HUMAN
Unclassified
---
A
D
12
V
15
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_04
*
G
12
V
RASK_HUMAN
Disease (Colorectal cancer)
---
A
D
12
V
16
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_05
*
G
12
V
RASK_HUMAN
Disease (Colorectal cancer)
---
A
D
12
V
17
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_06
*
G
12
V
RASK_HUMAN
Disease (Colorectal cancer)
---
A
D
12
V
18
UniProt
VAR_016029
G
13
D
RASK_HUMAN
Disease (GASC)
---
A
G
13
D
19
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_10
*
G
13
D
RASK_HUMAN
Disease (Colorectal cancer)
---
A
G
13
D
20
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_11
*
G
13
D
RASK_HUMAN
Disease (Colorectal cancer)
---
A
G
13
D
21
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_12
*
G
13
D
RASK_HUMAN
Disease (Colorectal cancer)
---
A
G
13
D
22
UniProt
VAR_065145
G
13
R
RASK_HUMAN
Unclassified
---
A
G
13
R
23
UniProt
VAR_026109
V
14
I
RASK_HUMAN
Disease (NS3)
---
A
V
14
I
24
UniProt
VAR_064850
Q
22
E
RASK_HUMAN
Disease (CFC2)
---
A
Q
22
E
25
UniProt
VAR_064851
Q
22
R
RASK_HUMAN
Disease (NS3)
---
A
Q
22
R
26
UniProt
VAR_064852
P
34
L
RASK_HUMAN
Disease (NS3)
---
A
P
34
L
27
UniProt
VAR_064853
P
34
Q
RASK_HUMAN
Disease (NS3)
---
A
P
34
Q
28
UniProt
VAR_026110
P
34
R
RASK_HUMAN
Disease (CFC2)
---
A
P
34
R
29
UniProt
VAR_064854
I
36
M
RASK_HUMAN
Disease (NS3)
---
A
I
36
M
30
UniProt
VAR_026111
T
58
I
RASK_HUMAN
Disease (NS3)
---
A
T
58
I
31
UniProt
VAR_016030
A
59
T
RASK_HUMAN
Disease (GASC)
---
A
A
59
T
32
UniProt
VAR_026112
G
60
R
RASK_HUMAN
Disease (CFC2)
---
A
G
60
R
33
UniProt
VAR_065146
G
60
S
RASK_HUMAN
Disease (NS3)
---
A
G
60
S
34
UniProt
VAR_006841
Q
61
H
RASK_HUMAN
Unclassified
17851045
A
Q
61
H
35
UniProt
VAR_036306
Q
61
R
RASK_HUMAN
Unclassified
---
A
Q
61
R
36
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_13
*
Q
61
R
RASK_HUMAN
Disease (Colorectal cancer)
---
A
Q
61
R
37
UniProt
VAR_069784
Y
71
H
RASK_HUMAN
Disease (CFC2)
---
A
Y
71
H
38
UniProt
VAR_036307
K
117
N
RASK_HUMAN
Unclassified
---
A
K
117
N
39
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_14
*
K
117
N
RASK_HUMAN
Disease (Colorectal cancer)
---
A
K
117
N
40
UniProt
VAR_036308
A
146
T
RASK_HUMAN
Unclassified
---
A
A
146
T
41
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_15
*
A
146
T
RASK_HUMAN
Disease (Colorectal cancer)
---
A
A
146
T
42
CancerSNP
VAR_RASK_HUMAN_CCDS8702_1_16
*
A
146
T
RASK_HUMAN
Disease (Colorectal cancer)
---
A
A
146
T
43
UniProt
VAR_069785
K
147
E
RASK_HUMAN
Disease (CFC2)
---
A
K
147
E
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RAS (A:2-180)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RAS
PS51421
small GTPase Ras family profile.
RASK_HUMAN
1-189
1
A:2-180
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.2a (A:1-37)
Exon 1.3 (A:38-97)
Exon 1.4 (A:97-150)
Exon 1.5b (A:151-180 (gaps))
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2a
2: Boundary 1.2a/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5b
5: Boundary 1.5b/1.6b
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
ENST00000256078
1
ENSE00001189804
chr12:
25403854-25403685
170
RASK_HUMAN
-
0
0
-
-
1.2a
ENST00000256078
2a
ENSE00000936617
chr12:
25398329-25398208
122
RASK_HUMAN
1-37
37
1
A:1-37
37
1.3
ENST00000256078
3
ENSE00001719809
chr12:
25380346-25380168
179
RASK_HUMAN
38-97
60
1
A:38-97
60
1.4
ENST00000256078
4
ENSE00001644818
chr12:
25378707-25378548
160
RASK_HUMAN
97-150
54
1
A:97-150
54
1.5b
ENST00000256078
5b
ENSE00001189807
chr12:
25368494-25368371
124
RASK_HUMAN
151-189
39
1
A:151-180 (gaps)
35
1.6b
ENST00000256078
6b
ENSE00001740851
chr12:
25362845-25358182
4664
RASK_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d4dsna_ (A:)
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
automated matches
(173)
Human (Homo sapiens) [TaxId: 9606]
(112)
1a
d4dsna_
A:
[
close SCOP info
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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:
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Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
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Nucleic
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Protein & NOT Site
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