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3VRZ
Asym. Unit
Info
Asym.Unit (154 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (77 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HCK COMPLEXED WITH A PYRROLO-PYRIMIDINE INHIBITOR 1-[4-(4-AMINO-7-CYCLOPENTYL-7H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)PHENYL]-3-BENZYLUREA
Authors
:
M. Kuratani, Y. Tomabechi, N. Handa, S. Yokoyama
Date
:
21 Apr 12 (Deposition) - 01 May 13 (Release) - 01 May 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.22
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Kinase, Transferase-Transferase Inhibitor Complex
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Gene Ontology, PubMed, Web (Google)
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Reference
:
Y. Saito, H. Yuki, M. Kuratani, Y. Hashizume, S. Takagi, T. Honma, A. Tanaka, M. Shirouzu, J. Mikuni, N. Handa, I. Ogahara, A. Sone, Y. Najima, Y. Tomabechi, M. Wakiyama, N. Uchida, M. Tomizawa-Murasawa, A. Kaneko, S. Tanaka, N. Suzuki, H. Kajita, Y. Aoki, O. Ohara, L. D. Shultz, T. Fukami, T. Goto, S. Taniguchi, S. Yokoyama, F. Ishikawa
A Pyrrolo-Pyrimidine Derivative Targets Human Primary Aml Stem Cells In Vivo
Sci Transl Med V. 5 1Ra52 2013
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: O-PHOSPHOTYROSINE (PTRa)
3b: O-PHOSPHOTYROSINE (PTRb)
4a: 1-[4-(4-AMINO-7-CYCLOPENTYL-7H-PYR... (VRZa)
4b: 1-[4-(4-AMINO-7-CYCLOPENTYL-7H-PYR... (VRZb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
CL
2
Ligand/Ion
CHLORIDE ION
3
PTR
2
Mod. Amino Acid
O-PHOSPHOTYROSINE
4
VRZ
2
Ligand/Ion
1-[4-(4-AMINO-7-CYCLOPENTYL-7H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)PHENYL]-3-BENZYLUREA
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:524 , PTR A:527 , HOH A:715 , GLU B:490
BINDING SITE FOR RESIDUE CA A 601
2
AC2
SOFTWARE
ARG A:85 , ARG A:123 , ARG A:128
BINDING SITE FOR RESIDUE CL A 602
3
AC3
SOFTWARE
LEU A:273 , VAL A:281 , ALA A:293 , PHE A:307 , MET A:314 , THR A:338 , GLU A:339 , MET A:341 , LEU A:393 , ASP A:404 , PHE A:405 , GLY A:406 , LEU A:407 , HOH A:708
BINDING SITE FOR RESIDUE VRZ A 603
4
AC4
SOFTWARE
GLU A:490 , GLU B:524 , PTR B:527 , HOH B:736
BINDING SITE FOR RESIDUE CA B 601
5
AC5
SOFTWARE
ARG B:85 , ARG B:123 , ARG B:128
BINDING SITE FOR RESIDUE CL B 602
6
AC6
SOFTWARE
LEU B:273 , VAL B:281 , ALA B:293 , PHE B:307 , LEU B:325 , THR B:338 , GLU B:339 , MET B:341 , LEU B:393 , ASP B:404 , PHE B:405 , HOH B:701 , HOH B:759
BINDING SITE FOR RESIDUE VRZ B 603
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SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_041708 (M110L, chain A/B, )
2: VAR_041709 (D404G, chain A/B, )
3: VAR_033836 (P507Q, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_041708
M
105
L
HCK_HUMAN
Polymorphism
55722810
A/B
M
110
L
2
UniProt
VAR_041709
D
399
G
HCK_HUMAN
Unclassified
---
A/B
D
404
G
3
UniProt
VAR_033836
P
502
Q
HCK_HUMAN
Polymorphism
17093828
A/B
P
507
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: SH2 (A:149-246,B:149-246)
2: PROTEIN_KINASE_ATP (A:273-295,B:273-295)
3: PROTEIN_KINASE_TYR (A:382-394,B:382-394)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SH2
PS50001
Src homology 2 (SH2) domain profile.
HCK_HUMAN
144-241
2
A:149-246
B:149-246
2
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
HCK_HUMAN
268-290
2
A:273-295
B:273-295
3
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
HCK_HUMAN
377-389
2
A:382-394
B:382-394
[
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Exons
(10, 20)
Info
All Exons
Exon 1.6a (A:85-115 | B:85-115)
Exon 1.7 (A:115-148 | B:115-148)
Exon 1.8 (A:148-183 | B:148-183)
Exon 1.9 (A:183-233 (gaps) | B:183-233 (gaps...)
Exon 1.10 (A:233-284 | B:233-284)
Exon 1.11 (A:284-344 | B:284-344)
Exon 1.12 (A:344-369 | B:344-369)
Exon 1.13 (A:370-411 | B:370-411)
Exon 1.14 (A:425-465 | B:424-465)
Exon 1.15d (A:465-531 | B:465-531)
View:
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All Exon Boundaries
01: Boundary 1.5/1.6a
02: Boundary 1.6a/1.7
03: Boundary 1.7/1.8
04: Boundary 1.8/1.9
05: Boundary 1.9/1.10
06: Boundary 1.10/1.11
07: Boundary 1.11/1.12
08: Boundary 1.12/1.13
09: Boundary 1.13/1.14
10: Boundary 1.14/1.15d
11: Boundary 1.15d/-
View:
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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
1.1c
ENST00000375852
1c
ENSE00002183369
chr20:
30640064-30640289
226
HCK_HUMAN
1-21
21
0
-
-
1.4a
ENST00000375852
4a
ENSE00001592701
chr20:
30659465-30659585
121
HCK_HUMAN
21-61
41
0
-
-
1.5
ENST00000375852
5
ENSE00000661152
chr20:
30661122-30661164
43
HCK_HUMAN
62-76
15
0
-
-
1.6a
ENST00000375852
6a
ENSE00000661153
chr20:
30661519-30661621
103
HCK_HUMAN
76-110
35
2
A:85-115
B:85-115
31
31
1.7
ENST00000375852
7
ENSE00000661154
chr20:
30662426-30662524
99
HCK_HUMAN
110-143
34
2
A:115-148
B:115-148
34
34
1.8
ENST00000375852
8
ENSE00000661155
chr20:
30667577-30667680
104
HCK_HUMAN
143-178
36
2
A:148-183
B:148-183
36
36
1.9
ENST00000375852
9
ENSE00000661156
chr20:
30671697-30671846
150
HCK_HUMAN
178-228
51
2
A:183-233 (gaps)
B:183-233 (gaps)
51
51
1.10
ENST00000375852
10
ENSE00000661157
chr20:
30672194-30672346
153
HCK_HUMAN
228-279
52
2
A:233-284
B:233-284
52
52
1.11
ENST00000375852
11
ENSE00000661158
chr20:
30674431-30674610
180
HCK_HUMAN
279-339
61
2
A:284-344
B:284-344
61
61
1.12
ENST00000375852
12
ENSE00000661159
chr20:
30676371-30676447
77
HCK_HUMAN
339-364
26
2
A:344-369
B:344-369
26
26
1.13
ENST00000375852
13
ENSE00001612642
chr20:
30681666-30681819
154
HCK_HUMAN
365-416
52
2
A:370-411
B:370-411
42
42
1.14
ENST00000375852
14
ENSE00001636203
chr20:
30686807-30686938
132
HCK_HUMAN
416-460
45
2
A:425-465
B:424-465
41
42
1.15d
ENST00000375852
15d
ENSE00001468583
chr20:
30689120-30689659
540
HCK_HUMAN
460-526
67
2
A:465-531
B:465-531
67
67
[
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SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d3vrza1 (A:85-146)
1b: SCOP_d3vrzb1 (B:85-146)
2a: SCOP_d3vrza3 (A:250-531)
2b: SCOP_d3vrzb3 (B:250-531)
3a: SCOP_d3vrza2 (A:147-249)
3b: SCOP_d3vrzb2 (B:147-249)
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Protein Domains
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(
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Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
SH3-like barrel
(1035)
Superfamily
:
SH3-domain
(369)
Family
:
SH3-domain
(255)
Protein domain
:
Hemapoetic cell kinase Hck
(20)
Human (Homo sapiens) [TaxId: 9606]
(20)
1a
d3vrza1
A:85-146
1b
d3vrzb1
B:85-146
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
:
Haemopoetic cell kinase Hck
(19)
Human (Homo sapiens) [TaxId: 9606]
(19)
2a
d3vrza3
A:250-531
2b
d3vrzb3
B:250-531
Fold
:
SH2-like
(260)
Superfamily
:
SH2 domain
(260)
Family
:
SH2 domain
(225)
Protein domain
:
Hemopoetic cell kinase Hck
(17)
Human (Homo sapiens) [TaxId: 9606]
(17)
3a
d3vrza2
A:147-249
3b
d3vrzb2
B:147-249
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (154 KB)
Header - Asym.Unit
Biol.Unit 1 (75 KB)
Header - Biol.Unit 1
Biol.Unit 2 (77 KB)
Header - Biol.Unit 2
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