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3CD0
Asym. Unit
Info
Asym.Unit (268 KB)
Biol.Unit 1 (261 KB)
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(1)
Title
:
THERMODYNAMIC AND STRUCTURE GUIDED DESIGN OF STATIN HMG-COA REDUCTASE INHIBITORS
Authors
:
A. Pavlovsky, R. W. Sarver, M. S. Harris, B. C. Finzel
Date
:
26 Feb 08 (Deposition) - 17 Jun 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase, Cholesterol Biosynthesis, Hmg-Coa, Nadph, Statin, Alternative Splicing, Endoplasmic Reticulum, Glycoprotein, Lipid Synthesis, Membrane, Peroxisome, Polymorphism, Steroid Biosynthesis, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. W. Sarver, E. Bills, G. Bolton, L. D. Bratton, N. L. Caspers, J. B. Dunbar, M. S. Harris, R. H. Hutchings, R. M. Kennedy, S. D. Larsen, A. Pavlovsky, J. A. Pfefferkorn, G. Bainbridge
Thermodynamic And Structure Guided Design Of Statin Based Inhibitors Of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase.
J. Med. Chem. V. 51 3804 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: (3R,5R)-7-{2-[(4-FLUOROBENZYL)CARB... (6HIa)
1b: (3R,5R)-7-{2-[(4-FLUOROBENZYL)CARB... (6HIb)
1c: (3R,5R)-7-{2-[(4-FLUOROBENZYL)CARB... (6HIc)
1d: (3R,5R)-7-{2-[(4-FLUOROBENZYL)CARB... (6HId)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6HI
4
Ligand/Ion
(3R,5R)-7-{2-[(4-FLUOROBENZYL)CARBAMOYL]-4-(4-FLUOROPHENYL)-1-(1-METHYLETHYL)-1H-IMIDAZOL-5-YL}-3,5-DIHYDROXYHEPTANOIC ACID
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:559 , GLY A:560 , ALA A:564 , SER A:565 , ARG A:568 , LYS A:735 , ALA A:751 , ASN A:755 , LEU A:853 , ALA A:856 , LEU A:857 , HIS A:861 , ARG B:590 , MET B:657 , SER B:661 , SER B:684 , ASN B:686 , ASP B:690 , LYS B:691 , LYS B:692 , HOH B:905 , HOH B:1042
BINDING SITE FOR RESIDUE 6HI B 1
2
AC2
SOFTWARE
ARG A:590 , SER A:661 , SER A:684 , ASN A:686 , ASP A:690 , LYS A:691 , LYS A:692 , GLU B:559 , GLY B:560 , ALA B:564 , SER B:565 , ARG B:568 , LYS B:735 , ALA B:751 , ASN B:755 , LEU B:853 , ALA B:856 , HOH B:879 , HOH B:1040
BINDING SITE FOR RESIDUE 6HI B 2
3
AC3
SOFTWARE
GLU C:559 , GLY C:560 , ALA C:564 , SER C:565 , LYS C:735 , ALA C:751 , HIS C:752 , ASN C:755 , LEU C:853 , ARG D:590 , MET D:657 , SER D:661 , SER D:684 , ASP D:690 , LYS D:691 , LYS D:692 , HOH D:890
BINDING SITE FOR RESIDUE 6HI D 3
4
AC4
SOFTWARE
ARG C:590 , SER C:684 , ASP C:690 , LYS C:691 , LYS C:692 , HOH C:880 , HOH C:970 , GLU D:559 , GLY D:560 , LEU D:562 , ALA D:564 , SER D:565 , ARG D:568 , LYS D:735 , ALA D:751 , ASN D:755 , LEU D:853 , ALA D:856 , HOH D:1041
BINDING SITE FOR RESIDUE 6HI C 4
[
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SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_011954 (I638V, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011954
I
638
V
HMDH_HUMAN
Polymorphism
5908
A/B/C/D
I
638
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 16)
Info
All PROSITE Patterns/Profiles
1: HMG_COA_REDUCTASE_4 (A:464-861,B:464-861,C:464-860,D:46...)
2: HMG_COA_REDUCTASE_1 (A:646-660,B:646-660,C:646-660,D:64...)
3: HMG_COA_REDUCTASE_2 (A:802-809,B:802-809,C:802-809,D:80...)
4: HMG_COA_REDUCTASE_3 (A:856-861,B:856-861,C:856-860,D:85...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HMG_COA_REDUCTASE_4
PS50065
Hydroxymethylglutaryl-coenzyme A reductases family profile.
HMDH_HUMAN
464-871
4
A:464-861
B:464-861
C:464-860
D:464-861
2
HMG_COA_REDUCTASE_1
PS00066
Hydroxymethylglutaryl-coenzyme A reductases signature 1.
HMDH_HUMAN
646-660
4
A:646-660
B:646-660
C:646-660
D:646-660
3
HMG_COA_REDUCTASE_2
PS00318
Hydroxymethylglutaryl-coenzyme A reductases signature 2.
HMDH_HUMAN
802-809
4
A:802-809
B:802-809
C:802-809
D:802-809
4
HMG_COA_REDUCTASE_3
PS01192
Hydroxymethylglutaryl-coenzyme A reductases signature 3.
HMDH_HUMAN
856-869
4
A:856-861
B:856-861
C:856-860
D:856-861
[
close PROSITE info
]
Exons
(9, 35)
Info
All Exons
Exon 1.13c (A:441-456 | B:441-456 | C:444-454 ...)
Exon 1.14c (A:457-521 | B:457-521 | C:458-521 ...)
Exon 1.15b (A:522-574 | B:522-574 | C:522-574 ...)
Exon 1.15d (A:575-627 | B:575-627 | C:575-627 ...)
Exon 1.16a (A:627-662 | B:627-662 | C:627-662 ...)
Exon 1.17b (A:663-719 | B:663-719 | C:663-719 ...)
Exon 1.18a (A:720-766 | B:720-766 | C:720-766 ...)
Exon 1.19a (A:767-819 | B:767-819 | C:767-819 ...)
Exon 1.20b (A:820-861 | B:820-861 | C:820-860 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.13a/1.13c
02: Boundary 1.13c/1.14c
03: Boundary 1.14c/1.15b
04: Boundary 1.15b/1.15d
05: Boundary 1.15d/1.16a
06: Boundary 1.16a/1.17b
07: Boundary 1.17b/1.18a
08: Boundary 1.18a/1.19a
09: Boundary 1.19a/1.20b
10: Boundary 1.20b/1.21g
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
1.2a
ENST00000287936
2a
ENSE00001378703
chr5:
74632993-74633125
133
HMDH_HUMAN
-
0
0
-
-
1.5b
ENST00000287936
5b
ENSE00002182886
chr5:
74638408-74638595
188
HMDH_HUMAN
1-55
55
0
-
-
1.6a
ENST00000287936
6a
ENSE00000753569
chr5:
74639678-74639789
112
HMDH_HUMAN
56-93
38
0
-
-
1.7b
ENST00000287936
7b
ENSE00000753572
chr5:
74640070-74640157
88
HMDH_HUMAN
93-122
30
0
-
-
1.8
ENST00000287936
8
ENSE00000753575
chr5:
74641399-74641483
85
HMDH_HUMAN
122-150
29
0
-
-
1.9
ENST00000287936
9
ENSE00000753578
chr5:
74643029-74643134
106
HMDH_HUMAN
151-186
36
0
-
-
1.10b
ENST00000287936
10b
ENSE00000753581
chr5:
74645867-74645973
107
HMDH_HUMAN
186-221
36
0
-
-
1.11
ENST00000287936
11
ENSE00000753584
chr5:
74646083-74646199
117
HMDH_HUMAN
222-260
39
0
-
-
1.12
ENST00000287936
12
ENSE00000753587
chr5:
74646614-74646774
161
HMDH_HUMAN
261-314
54
0
-
-
1.13a
ENST00000287936
13a
ENSE00000753589
chr5:
74646893-74647140
248
HMDH_HUMAN
314-397
84
0
-
-
1.13c
ENST00000287936
13c
ENSE00000753591
chr5:
74647249-74647427
179
HMDH_HUMAN
397-456
60
3
A:441-456
B:441-456
C:444-454
-
16
16
11
-
1.14c
ENST00000287936
14c
ENSE00000753593
chr5:
74650328-74650522
195
HMDH_HUMAN
457-521
65
4
A:457-521
B:457-521
C:458-521
D:458-521 (gaps)
65
65
64
64
1.15b
ENST00000287936
15b
ENSE00000753595
chr5:
74650881-74651039
159
HMDH_HUMAN
522-574
53
4
A:522-574
B:522-574
C:522-574
D:522-574
53
53
53
53
1.15d
ENST00000287936
15d
ENSE00000753597
chr5:
74651190-74651347
158
HMDH_HUMAN
575-627
53
4
A:575-627
B:575-627
C:575-627
D:575-627
53
53
53
53
1.16a
ENST00000287936
16a
ENSE00000753599
chr5:
74652168-74652273
106
HMDH_HUMAN
627-662
36
4
A:627-662
B:627-662
C:627-662
D:627-662
36
36
36
36
1.17b
ENST00000287936
17b
ENSE00000753601
chr5:
74654482-74654652
171
HMDH_HUMAN
663-719
57
4
A:663-719
B:663-719
C:663-719
D:663-719
57
57
57
57
1.18a
ENST00000287936
18a
ENSE00000753603
chr5:
74654995-74655135
141
HMDH_HUMAN
720-766
47
4
A:720-766
B:720-766
C:720-766
D:720-766
47
47
47
47
1.19a
ENST00000287936
19a
ENSE00000753605
chr5:
74655223-74655381
159
HMDH_HUMAN
767-819
53
4
A:767-819
B:767-819
C:767-819
D:767-819
53
53
53
53
1.20b
ENST00000287936
20b
ENSE00000753607
chr5:
74655810-74655964
155
HMDH_HUMAN
820-871
52
4
A:820-861
B:820-861
C:820-860
D:820-861
42
42
41
42
1.21g
ENST00000287936
21g
ENSE00001859900
chr5:
74656113-74657929
1817
HMDH_HUMAN
871-888
18
0
-
-
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_3cd0A03 (A:587-703)
1b: CATH_3cd0B03 (B:587-703)
1c: CATH_3cd0C03 (C:587-703)
1d: CATH_3cd0D03 (D:587-703)
2a: CATH_3cd0A02 (A:537-585,A:704-861)
2b: CATH_3cd0B02 (B:537-585,B:704-861)
2c: CATH_3cd0D02 (D:537-585,D:704-861)
2d: CATH_3cd0C02 (C:537-585,C:704-860)
3a: CATH_3cd0D01 (D:458-536)
3b: CATH_3cd0A01 (A:462-536)
3c: CATH_3cd0B01 (B:462-536)
3d: CATH_3cd0C01 (C:462-536)
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.420, no name defined]
(27)
Human (Homo sapiens)
(22)
1a
3cd0A03
A:587-703
1b
3cd0B03
B:587-703
1c
3cd0C03
C:587-703
1d
3cd0D03
D:587-703
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2
(27)
Homologous Superfamily
:
3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2
(27)
Human (Homo sapiens)
(22)
2a
3cd0A02
A:537-585,A:704-861
2b
3cd0B02
B:537-585,B:704-861
2c
3cd0D02
D:537-585,D:704-861
2d
3cd0C02
C:537-585,C:704-860
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
HMGR, N-terminal domain
(22)
Homologous Superfamily
:
HMGR, N-terminal domain
(22)
Human (Homo sapiens)
(22)
3a
3cd0D01
D:458-536
3b
3cd0A01
A:462-536
3c
3cd0B01
B:462-536
3d
3cd0C01
C:462-536
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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