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3QCX
Asym. Unit
Info
Asym.Unit (55 KB)
Biol.Unit 1 (50 KB)
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(1)
Title
:
PHOSPHOINOSITIDE-DEPENDENT KINASE-1 (PDK1) KINASE DOMAIN WITH 6-{2-AMINO-6-[(3R)-3-METHYL-4-MORPHOLINYL]-4-PYRIMIDINYL}-1H-INDAZOL-3-AMINE
Authors
:
J. R. Medina, C. J. Becker, C. W. Blackledge, C. Duquenne, Y. Feng, S. W. G D. Heerding, W. H. Li, W. H. Miller, S. P. Romeril, D. Scherzer, A. Shu, M A. R. Chadderton, M. Dumble, C. M. Gradiner, S. Gilbert, Q. Liu, S. K. Ra V. Sudakin, H. Xiang, P. G. Brady, N. Campobasso, P. Ward, J. M. Axten
Date
:
17 Jan 11 (Deposition) - 09 Mar 11 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Kinase Domain, Agc Kinase, Signal Transduction, Phosphorylation On S241, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Medina, C. J. Becker, C. W. Blackledge, C. Duquenne, Y. Feng, S. W. Grant, D. Heerding, W. H. Li, W. H. Miller, S. P. Romeril, D. Scherzer, A. Shu, M. A. Bobko, A. R. Chadderton, M. Dumble, C. M. Gardiner, S. Gilbert, Q. Liu, S. K. Rabindran, V. Sudakin, H. Xiang, P. G. Brady, N. Campobasso, P. Ward, J. M. Axten
Structure-Based Design Of Potent And Selective 3-Phosphoinositide-Dependent Kinase-1 (Pdk1) Inhibitors.
J. Med. Chem. V. 54 1871 2011
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 13)
Info
All Hetero Components
1a: 6-{2-AMINO-6-[(3R)-3-METHYLMORPHOL... (3Q2a)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: PHOSPHOSERINE (SEPa)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3Q2
1
Ligand/Ion
6-{2-AMINO-6-[(3R)-3-METHYLMORPHOLIN-4-YL]PYRIMIDIN-4-YL}-2H-INDAZOL-3-AMINE
2
GOL
5
Ligand/Ion
GLYCEROL
3
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
4
SO4
6
Ligand/Ion
SULFATE ION
[
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Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SO4 A:1 , SO4 A:2 , SO4 A:3 , ARG A:106 , GLU A:107 , SER A:160 , TYR A:161
BINDING SITE FOR RESIDUE GOL A 360
02
AC2
SOFTWARE
PHE A:82 , LYS A:83 , PHE A:84 , GLU A:194 , LYS A:337 , HOH A:386
BINDING SITE FOR RESIDUE GOL A 361
03
AC3
SOFTWARE
PRO A:79 , LYS A:154 , TYR A:156 , GLU A:331 , GLY A:332
BINDING SITE FOR RESIDUE GOL A 363
04
AC4
SOFTWARE
ALA A:103 , THR A:104 , SER A:105 , HIS A:139 , SER A:191 , TRP A:347 , GLU A:348 , ASN A:349 , LEU A:350 , HIS A:351
BINDING SITE FOR RESIDUE GOL A 365
05
AC5
SOFTWARE
LYS A:83 , VAL A:345 , THR A:346 , TRP A:347 , GLU A:348
BINDING SITE FOR RESIDUE SO4 A 366
06
AC6
SOFTWARE
GLN A:73 , PRO A:74 , ARG A:75 , ARG A:136 , LYS A:199
BINDING SITE FOR RESIDUE SO4 A 368
07
AC7
SOFTWARE
LYS A:76 , ARG A:131 , THR A:148 , PHE A:149 , GLN A:150
BINDING SITE FOR RESIDUE SO4 A 369
08
AC8
SOFTWARE
SO4 A:2 , SER A:105 , ARG A:106 , GLU A:107 , HIS A:351 , GLN A:352 , GOL A:360
BINDING SITE FOR RESIDUE SO4 A 1
09
AC9
SOFTWARE
SO4 A:1 , ARG A:106 , PRO A:140 , HIS A:351 , GOL A:360
BINDING SITE FOR RESIDUE SO4 A 2
10
BC1
SOFTWARE
TYR A:146 , SER A:160 , GLN A:220 , GOL A:360
BINDING SITE FOR RESIDUE SO4 A 3
11
BC2
SOFTWARE
GLU A:90 , GLY A:91 , ALA A:109 , LYS A:111 , GLU A:130 , LEU A:159 , SER A:160 , TYR A:161 , ALA A:162 , LEU A:212 , THR A:222 , ASP A:223 , GOL A:362
BINDING SITE FOR RESIDUE 3Q2 A 370
12
BC3
SOFTWARE
LYS A:111 , TYR A:126 , GLU A:130 , GLY A:225 , 3Q2 A:370 , HOH A:383 , HOH A:396
BINDING SITE FOR RESIDUE GOL A 362
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:88-111)
2: PROTEIN_KINASE_ST (A:201-213)
;
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.
PDPK1_HUMAN
88-111
1
A:88-111
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
PDPK1_HUMAN
201-213
1
A:201-213
[
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Exons
(9, 9)
Info
All Exons
Exon 1.6c (A:73-95)
Exon 1.7 (A:96-110)
Exon 1.8b (A:110-156)
Exon 1.9b (A:156-204)
Exon 1.10a (A:204-231)
Exon 1.13 (A:241-262)
Exon 1.14 (A:262-285)
Exon 1.15b (A:285-317)
Exon 1.16a (A:318-358)
View:
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All Exon Boundaries
01: Boundary 1.1a/1.6c
02: Boundary 1.6c/1.7
03: Boundary 1.7/1.8b
04: Boundary 1.8b/1.9b
05: Boundary 1.9b/1.10a
06: Boundary 1.10a/1.13
07: Boundary 1.13/1.14
08: Boundary 1.14/1.15b
09: Boundary 1.15b/1.16a
10: Boundary 1.16a/1.17
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
ENST00000342085
1a
ENSE00001944688
chr16:
2587965-2588137
173
PDPK1_HUMAN
1-8
8
0
-
-
1.6c
ENST00000342085
6c
ENSE00001640744
chr16:
2607704-2607964
261
PDPK1_HUMAN
9-95
87
1
A:73-95
23
1.7
ENST00000342085
7
ENSE00001620065
chr16:
2611481-2611523
43
PDPK1_HUMAN
96-110
15
1
A:96-110
15
1.8b
ENST00000342085
8b
ENSE00001694535
chr16:
2611772-2611909
138
PDPK1_HUMAN
110-156
47
1
A:110-156
47
1.9b
ENST00000342085
9b
ENSE00001744256
chr16:
2615554-2615698
145
PDPK1_HUMAN
156-204
49
1
A:156-204
49
1.10a
ENST00000342085
10a
ENSE00001705748
chr16:
2616357-2616454
98
PDPK1_HUMAN
204-237
34
1
A:204-231
28
1.13
ENST00000342085
13
ENSE00001704745
chr16:
2627426-2627501
76
PDPK1_HUMAN
237-262
26
1
A:241-262
22
1.14
ENST00000342085
14
ENSE00001686272
chr16:
2631296-2631364
69
PDPK1_HUMAN
262-285
24
1
A:262-285
24
1.15b
ENST00000342085
15b
ENSE00001743545
chr16:
2631608-2631704
97
PDPK1_HUMAN
285-317
33
1
A:285-317
33
1.16a
ENST00000342085
16a
ENSE00001314244
chr16:
2633413-2633586
174
PDPK1_HUMAN
318-375
58
1
A:318-358
41
1.17
ENST00000342085
17
ENSE00000946017
chr16:
2636677-2636894
218
PDPK1_HUMAN
376-448
73
0
-
-
1.18
ENST00000342085
18
ENSE00000946018
chr16:
2645794-2645851
58
PDPK1_HUMAN
448-467
20
0
-
-
1.19
ENST00000342085
19
ENSE00000946019
chr16:
2647124-2647276
153
PDPK1_HUMAN
468-518
51
0
-
-
1.20b
ENST00000342085
20b
ENSE00001505218
chr16:
2647652-2653189
5538
PDPK1_HUMAN
519-556
38
0
-
-
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3qcxa_ (A:)
View:
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Classes
(
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(
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Folds
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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
:
automated matches
(529)
Protein domain
:
automated matches
(529)
Human (Homo sapiens) [TaxId: 9606]
(438)
1a
d3qcxa_
A:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Pkinase_3qcxA01 (A:82-341)
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Clans
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Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
1a
Pkinase-3qcxA01
A:82-341
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Asymmetric Unit 1
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