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3ZIM
Asym. Unit
Info
Asym.Unit (322 KB)
Biol.Unit 1 (314 KB)
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(1)
Title
:
DISCOVERY OF A POTENT AND ISOFORM-SELECTIVE TARGETED COVALENT INHIBITOR OF THE LIPID KINASE PI3KALPHA
Authors
:
M. Nacht, L. Qiao, M. P. Sheets, T. S. Martin, M. Labenski, H. Mazdiyasni Z. Zhu, P. Chaturvedi, D. Bhavsar, D. Niu, W. Westlin, R. C. Petter, A. P. Medikonda, A. Jestel, M. Blaesse, J. Singh
Date
:
09 Jan 13 (Deposition) - 13 Feb 13 (Release) - 27 Feb 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Nacht, L. Qiao, M. P. Sheets, T. S. Martin, M. Labenski, H. Mazdiyasni, R. Karp, Z. Zhu, P. Chaturvedi, D. Bhavsar, D. Niu, W. Westlin, R. C. Petter, A. P. Medikonda, J. Singh
Discovery Of A Potent And Isoform-Selective Targeted Covalent Inhibitor Of The Lipid Kinase Pi3Kalpha
J. Med. Chem. V. 56 712 2013
[
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]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: 1-[4-[[2-(1H-INDAZOL-4-YL)-4-MORPH... (KKRa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
KKR
1
Ligand/Ion
1-[4-[[2-(1H-INDAZOL-4-YL)-4-MORPHOLIN-4-YL-THIENO[3,2-D]PYRIMIDIN-6-YL]METHYL]PIPERAZIN-1-YL]-6-METHYL-HEPT-5-ENE-1,4-DIONE
[
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET A:772 , ILE A:800 , LYS A:802 , ASP A:810 , TYR A:836 , ILE A:848 , GLU A:849 , VAL A:850 , VAL A:851 , SER A:854 , MET A:858 , GLN A:859 , CYS A:862 , ILE A:932 , ASP A:933
BINDING SITE FOR RESIDUE KKR A2047
[
close Site info
]
SAPs(SNPs)/Variants
(34, 34)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_069786 (G118D, chain A, )
02: VAR_069787 (E135K, chain A, )
03: VAR_069788 (E218K, chain A, )
04: VAR_042943 (S332R, chain A, )
05: VAR_026169 (Y343C, chain A, )
06: VAR_069789 (V356I, chain A, )
07: VAR_069252 (G364R, chain A, )
08: VAR_069253 (E365K, chain A, )
09: VAR_069254 (C378Y, chain A, )
10: VAR_069790 (R382K, chain A, )
11: VAR_026170 (I391M, chain A, )
12: VAR_026171 (C420R, chain A, )
13: VAR_026172 (E453Q, chain A, )
14: VAR_026173 (E542K, chain A, )
15: VAR_026174 (E542Q, chain A, )
16: VAR_026175 (E542V, chain A, )
17: VAR_026176 (E545A, chain A, )
18: VAR_026177 (E545G, chain A, )
19: VAR_026178 (E545K, chain A, )
20: VAR_026179 (Q546E, chain A, )
21: VAR_026180 (Q546K, chain A, )
22: VAR_026181 (Q546P, chain A, )
23: VAR_026182 (Q546R, chain A, )
24: VAR_069256 (E726K, chain A, )
25: VAR_069257 (G914R, chain A, )
26: VAR_026183 (G1007R, chain A, )
27: VAR_026184 (Y1021C, chain A, )
28: VAR_026185 (Y1021H, chain A, )
29: VAR_026186 (Y1021N, chain A, )
30: VAR_026187 (R1023Q, chain A, )
31: VAR_069258 (T1025A, chain A, )
32: VAR_026188 (T1025N, chain A, )
33: VAR_026189 (A1035V, chain A, )
34: VAR_026190 (M1043I, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_069786
G
118
D
PK3CA_HUMAN
Disease (CWS5)
---
A
G
118
D
02
UniProt
VAR_069787
E
135
K
PK3CA_HUMAN
Disease (CWS5)
---
A
E
135
K
03
UniProt
VAR_069788
E
218
K
PK3CA_HUMAN
Disease (CWS5)
---
A
E
218
K
04
UniProt
VAR_042943
S
332
R
PK3CA_HUMAN
Polymorphism
1051407
A
S
332
R
05
UniProt
VAR_026169
Y
343
C
PK3CA_HUMAN
Unclassified
---
A
Y
343
C
06
UniProt
VAR_069789
V
356
I
PK3CA_HUMAN
Disease (CWS5)
---
A
V
356
I
07
UniProt
VAR_069252
G
364
R
PK3CA_HUMAN
Disease (MCAP)
---
A
G
364
R
08
UniProt
VAR_069253
E
365
K
PK3CA_HUMAN
Disease (MCAP)
---
A
E
365
K
09
UniProt
VAR_069254
C
378
Y
PK3CA_HUMAN
Disease (MCAP)
---
A
C
378
Y
10
UniProt
VAR_069790
R
382
K
PK3CA_HUMAN
Disease (CWS5)
---
A
R
382
K
11
UniProt
VAR_026170
I
391
M
PK3CA_HUMAN
Polymorphism
3729680
A
I
391
M
12
UniProt
VAR_026171
C
420
R
PK3CA_HUMAN
Disease (CLOVE)
---
A
C
420
R
13
UniProt
VAR_026172
E
453
Q
PK3CA_HUMAN
Disease (CRC)
---
A
E
453
Q
14
UniProt
VAR_026173
E
542
K
PK3CA_HUMAN
Disease (KERSEB)
---
A
E
542
K
15
UniProt
VAR_026174
E
542
Q
PK3CA_HUMAN
Unclassified
---
A
E
542
Q
16
UniProt
VAR_026175
E
542
V
PK3CA_HUMAN
Unclassified
---
A
E
542
V
17
UniProt
VAR_026176
E
545
A
PK3CA_HUMAN
Disease (HCC)
---
A
E
545
A
18
UniProt
VAR_026177
E
545
G
PK3CA_HUMAN
Disease (KERSEB)
---
A
E
545
G
19
UniProt
VAR_026178
E
545
K
PK3CA_HUMAN
Disease (MCAP)
---
A
E
545
K
20
UniProt
VAR_026179
Q
546
E
PK3CA_HUMAN
Unclassified
---
A
Q
546
E
21
UniProt
VAR_026180
Q
546
K
PK3CA_HUMAN
Unclassified
---
A
Q
546
K
22
UniProt
VAR_026181
Q
546
P
PK3CA_HUMAN
Unclassified
---
A
Q
546
P
23
UniProt
VAR_026182
Q
546
R
PK3CA_HUMAN
Unclassified
---
A
Q
546
R
24
UniProt
VAR_069256
E
726
K
PK3CA_HUMAN
Disease (MCAP)
---
A
E
726
K
25
UniProt
VAR_069257
G
914
R
PK3CA_HUMAN
Disease (MCAP)
---
A
G
914
R
26
UniProt
VAR_026183
G
1007
R
PK3CA_HUMAN
Unclassified
---
A
G
1007
R
27
UniProt
VAR_026184
Y
1021
C
PK3CA_HUMAN
Disease (MCAP)
---
A
Y
1021
C
28
UniProt
VAR_026185
Y
1021
H
PK3CA_HUMAN
Unclassified
---
A
Y
1021
H
29
UniProt
VAR_026186
Y
1021
N
PK3CA_HUMAN
Unclassified
---
A
Y
1021
N
30
UniProt
VAR_026187
R
1023
Q
PK3CA_HUMAN
Unclassified
---
A
R
1023
Q
31
UniProt
VAR_069258
T
1025
A
PK3CA_HUMAN
Disease (MCAP)
---
A
T
1025
A
32
UniProt
VAR_026188
T
1025
N
PK3CA_HUMAN
Unclassified
---
A
T
1025
N
33
UniProt
VAR_026189
A
1035
V
PK3CA_HUMAN
Disease (MCAP)
---
A
A
1035
V
34
UniProt
VAR_026190
M
1043
I
PK3CA_HUMAN
Disease (MCAP)
---
A
M
1043
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(6, 6)
Info
All PROSITE Patterns/Profiles
1: PI3K_RBD (A:187-289)
2: PI3K_C2 (A:330-487)
3: PIK_HELICAL (A:517-694)
4: PI3_4_KINASE_3 (A:797-1046)
5: PI3_4_KINASE_1 (A:801-815)
6: PI3_4_KINASE_2 (A:900-920)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PI3K_RBD
PS51546
Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile.
PK3CA_HUMAN
187-289
1
A:187-289
2
PI3K_C2
PS51547
Phosphatidylinositol 3-kinase C2 (PI3K C2) domain profile.
PK3CA_HUMAN
330-487
1
A:330-487
3
PIK_HELICAL
PS51545
PIK helical domain profile.
PK3CA_HUMAN
517-694
1
A:517-694
4
PI3_4_KINASE_3
PS50290
Phosphatidylinositol 3- and 4-kinases family profile.
PK3CA_HUMAN
797-1068
1
A:797-1046
5
PI3_4_KINASE_1
PS00915
Phosphatidylinositol 3- and 4-kinases signature 1.
PK3CA_HUMAN
801-815
1
A:801-815
6
PI3_4_KINASE_2
PS00916
Phosphatidylinositol 3- and 4-kinases signature 2.
PK3CA_HUMAN
900-920
1
A:900-920
[
close PROSITE info
]
Exons
(20, 20)
Info
All Exons
Exon 1.4b (A:107-118)
Exon 1.5 (A:118-188)
Exon 1.6 (A:188-271 (gaps))
Exon 1.7 (A:272-353 (gaps))
Exon 1.8 (A:354-382)
Exon 1.9 (A:382-408)
Exon 1.10 (A:419-468)
Exon 1.11 (A:469-513)
Exon 1.12 (A:514-555)
Exon 1.13 (A:555-582)
Exon 1.14b (A:583-637)
Exon 1.15 (A:638-672)
Exon 1.16 (A:672-729)
Exon 1.17 (A:730-765)
Exon 1.18 (A:765-806)
Exon 1.19b (A:806-832)
Exon 1.20 (A:832-889)
Exon 1.21 (A:889-928)
Exon 1.22 (A:929-979 (gaps))
Exon 1.23 (A:979-1046)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2/1.4b
02: Boundary 1.4b/1.5
03: Boundary 1.5/1.6
04: Boundary 1.6/1.7
05: Boundary 1.7/1.8
06: Boundary 1.8/1.9
07: Boundary 1.9/1.10
08: Boundary 1.10/1.11
09: Boundary 1.11/1.12
10: Boundary 1.12/1.13
11: Boundary 1.13/1.14b
12: Boundary 1.14b/1.15
13: Boundary 1.15/1.16
14: Boundary 1.16/1.17
15: Boundary 1.17/1.18
16: Boundary 1.18/1.19b
17: Boundary 1.19b/1.20
18: Boundary 1.20/1.21
19: Boundary 1.21/1.22
20: Boundary 1.22/1.23
21: Boundary 1.23/-
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
1.2
ENST00000263967
2
ENSE00001493081
chr3:
178866311-178866391
81
PK3CA_HUMAN
-
0
0
-
-
1.4b
ENST00000263967
4b
ENSE00001139995
chr3:
178916538-178916965
428
PK3CA_HUMAN
1-118
118
1
A:107-118
12
1.5
ENST00000263967
5
ENSE00000997375
chr3:
178917478-178917687
210
PK3CA_HUMAN
118-188
71
1
A:118-188
71
1.6
ENST00000263967
6
ENSE00001077693
chr3:
178919078-178919328
251
PK3CA_HUMAN
188-271
84
1
A:188-271 (gaps)
84
1.7
ENST00000263967
7
ENSE00001077692
chr3:
178921332-178921577
246
PK3CA_HUMAN
272-353
82
1
A:272-353 (gaps)
82
1.8
ENST00000263967
8
ENSE00001077694
chr3:
178922291-178922376
86
PK3CA_HUMAN
354-382
29
1
A:354-382
29
1.9
ENST00000263967
9
ENSE00001077691
chr3:
178927383-178927488
106
PK3CA_HUMAN
382-417
36
1
A:382-408
27
1.10
ENST00000263967
10
ENSE00001128470
chr3:
178927974-178928126
153
PK3CA_HUMAN
418-468
51
1
A:419-468
50
1.11
ENST00000263967
11
ENSE00001128465
chr3:
178928219-178928353
135
PK3CA_HUMAN
469-513
45
1
A:469-513
45
1.12
ENST00000263967
12
ENSE00001077674
chr3:
178935998-178936122
125
PK3CA_HUMAN
514-555
42
1
A:514-555
42
1.13
ENST00000263967
13
ENSE00000826291
chr3:
178936984-178937065
82
PK3CA_HUMAN
555-582
28
1
A:555-582
28
1.14b
ENST00000263967
14b
ENSE00000826292
chr3:
178937359-178937523
165
PK3CA_HUMAN
583-637
55
1
A:583-637
55
1.15
ENST00000263967
15
ENSE00000826293
chr3:
178937737-178937840
104
PK3CA_HUMAN
638-672
35
1
A:638-672
35
1.16
ENST00000263967
16
ENSE00000826294
chr3:
178938774-178938945
172
PK3CA_HUMAN
672-729
58
1
A:672-729
58
1.17
ENST00000263967
17
ENSE00000826295
chr3:
178941869-178941975
107
PK3CA_HUMAN
730-765
36
1
A:730-765
36
1.18
ENST00000263967
18
ENSE00000826296
chr3:
178942488-178942609
122
PK3CA_HUMAN
765-806
42
1
A:765-806
42
1.19b
ENST00000263967
19b
ENSE00000826297
chr3:
178943750-178943828
79
PK3CA_HUMAN
806-832
27
1
A:806-832
27
1.20
ENST00000263967
20
ENSE00000826298
chr3:
178947060-178947230
171
PK3CA_HUMAN
832-889
58
1
A:832-889
58
1.21
ENST00000263967
21
ENSE00000826299
chr3:
178947792-178947909
118
PK3CA_HUMAN
889-928
40
1
A:889-928
40
1.22
ENST00000263967
22
ENSE00000826300
chr3:
178948013-178948164
152
PK3CA_HUMAN
929-979
51
1
A:929-979 (gaps)
51
1.23
ENST00000263967
23
ENSE00001139987
chr3:
178951882-178957881
6000
PK3CA_HUMAN
979-1068
90
1
A:979-1046
68
[
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SCOP Domains
(0, 0)
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All SCOP Domains
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all CATH domains
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Pfam Domains
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all PFAM domains
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