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3D4N
Asym. Unit
Info
Asym.Unit (179 KB)
Biol.Unit 1 (88 KB)
Biol.Unit 2 (88 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN 11-BETA-HYDROXYSTEROID DEHYDROGENASE (HSD1) IN COMPLEX WITH SULFONAMIDE INHIBITOR
Authors
:
Z. Wang, J. Liu, A. Sudom, N. P. Walker
Date
:
14 May 08 (Deposition) - 22 Jul 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Oxidoreductase, 11Beta, Hydroxysteroid, Dehydrogenase, Endoplasmic Reticulum, Glycoprotein, Lipid Metabolism, Membrane, Microsome, Nadp, Polymorphism, Signal-Anchor, Steroid Metabolism, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. D. Julian, Z. Wang, T. Bostick, S. Caille, R. Choi, M. Degraffenreid, Y. Di, X. He, R. W. Hungate, J. C. Jaen, J. Liu, M. Monshouwer, D. Mcminn, Y. Rew, A. Sudom, D. Sun, H. Tu, S. Ursu, N. Walker, X. Yan, Q. Ye, J. P. Powers
Discovery Of Novel, Potent Benzamide Inhibitors Of 11Beta-Hydroxysteroid Dehydrogenase Type 1 (11Beta-Hsd1) Exhibiting Oral Activity In An Enzyme Inhibition Ex Vivo Model
J. Med. Chem. V. 51 3953 2008
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: 1-{[(3R)-3-METHYL-4-({4-[(1S)-2,2,... (D4Na)
1b: 1-{[(3R)-3-METHYL-4-({4-[(1S)-2,2,... (D4Nb)
1c: 1-{[(3R)-3-METHYL-4-({4-[(1S)-2,2,... (D4Nc)
1d: 1-{[(3R)-3-METHYL-4-({4-[(1S)-2,2,... (D4Nd)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
2c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
2d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
D4N
4
Ligand/Ion
1-{[(3R)-3-METHYL-4-({4-[(1S)-2,2,2-TRIFLUORO-1-HYDROXY-1-METHYLETHYL]PHENYL}SULFONYL)PIPERAZIN-1-YL]METHYL}CYCLOPROPANECARBOXAMIDE
2
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:41 , SER A:43 , GLY A:45 , ILE A:46 , ARG A:66 , SER A:67 , THR A:92 , MET A:93 , ASN A:119 , ILE A:121 , SER A:169 , SER A:170 , TYR A:183 , LYS A:187 , LEU A:215 , GLY A:216 , LEU A:217 , ILE A:218 , THR A:220 , THR A:222 , ALA A:223
BINDING SITE FOR RESIDUE NAP A 1
2
AC2
SOFTWARE
GLY B:41 , SER B:43 , LYS B:44 , GLY B:45 , ILE B:46 , ALA B:65 , ARG B:66 , SER B:67 , THR B:92 , MET B:93 , ASN B:119 , HIS B:120 , ILE B:121 , SER B:170 , TYR B:183 , LYS B:187 , LEU B:215 , GLY B:216 , LEU B:217 , ILE B:218 , THR B:220 , THR B:222 , ALA B:223
BINDING SITE FOR RESIDUE NAP B 2
3
AC3
SOFTWARE
GLY C:41 , SER C:43 , LYS C:44 , GLY C:45 , ILE C:46 , ALA C:65 , ARG C:66 , SER C:67 , THR C:92 , MET C:93 , ASN C:119 , HIS C:120 , ILE C:121 , SER C:169 , SER C:170 , TYR C:183 , LYS C:187 , LEU C:215 , GLY C:216 , LEU C:217 , ILE C:218 , THR C:220 , THR C:222 , ALA C:223
BINDING SITE FOR RESIDUE NAP C 3
4
AC4
SOFTWARE
GLY D:41 , SER D:43 , LYS D:44 , GLY D:45 , ILE D:46 , ALA D:65 , ARG D:66 , SER D:67 , THR D:92 , MET D:93 , ASN D:119 , HIS D:120 , ILE D:121 , SER D:169 , SER D:170 , TYR D:183 , LYS D:187 , LEU D:215 , GLY D:216 , LEU D:217 , ILE D:218 , THR D:220 , THR D:222 , ALA D:223
BINDING SITE FOR RESIDUE NAP D 4
5
AC5
SOFTWARE
THR A:124 , SER A:170 , LEU A:171 , ALA A:172 , TYR A:177 , PRO A:178 , TYR A:183 , LEU A:215 , GLY A:216 , ALA A:226 , MET A:233
BINDING SITE FOR RESIDUE D4N A 293
6
AC6
SOFTWARE
THR B:124 , SER B:170 , LEU B:171 , ALA B:172 , TYR B:177 , PRO B:178 , TYR B:183 , LEU B:215 , GLY B:216 , LEU B:217 , ALA B:223 , ALA B:226
BINDING SITE FOR RESIDUE D4N B 293
7
AC7
SOFTWARE
THR C:124 , SER C:125 , LEU C:126 , SER C:170 , LEU C:171 , ALA C:172 , PRO C:178 , TYR C:183 , LEU C:215 , GLY C:216 , LEU C:217 , ALA C:223 , ALA C:226
BINDING SITE FOR RESIDUE D4N C 293
8
AC8
SOFTWARE
THR D:124 , SER D:125 , LEU D:126 , SER D:170 , LEU D:171 , ALA D:172 , PRO D:178 , TYR D:183 , LEU D:215 , GLY D:216 , ALA D:223 , ALA D:226
BINDING SITE FOR RESIDUE D4N D 293
[
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SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_035845 (V148E, chain A/B/C/D, )
2: VAR_DHI1_HUMAN_CCDS1489_1_01 (V148E, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_035845
V
148
E
DHI1_HUMAN
Unclassified
---
A/B/C/D
V
148
E
2
CancerSNP
VAR_DHI1_HUMAN_CCDS1489_1_01
*
V
148
E
DHI1_HUMAN
Disease (Breast cancer)
---
A/B/C/D
V
148
E
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ADH_SHORT (A:170-198,B:170-198,C:170-198,D:17...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_SHORT
PS00061
Short-chain dehydrogenases/reductases family signature.
DHI1_HUMAN
170-198
4
A:170-198
B:170-198
C:170-198
D:170-198
[
close PROSITE info
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Exons
(6, 24)
Info
All Exons
Exon 1.2b (A:21-30 | B:20-30 | C:20-30 | D:20...)
Exon 1.3 (A:30-73 | B:30-73 | C:30-73 | D:30...)
Exon 1.4 (A:74-111 | B:74-111 | C:74-111 | D...)
Exon 1.5 (A:111-173 | B:111-173 | C:111-173 ...)
Exon 1.6 (A:173-221 | B:173-221 | C:173-221 ...)
Exon 1.7a (A:221-282 (gaps) | B:221-284 | C:2...)
View:
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All Exon Boundaries
1: Boundary 1.1a/1.2b
2: Boundary 1.2b/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7a
7: Boundary 1.7a/-
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
1.1a
ENST00000367028
1a
ENSE00001443288
chr1:
209859510-209859630
121
DHI1_HUMAN
-
0
0
-
-
1.2b
ENST00000367028
2b
ENSE00001443287
chr1:
209878240-209878375
136
DHI1_HUMAN
1-30
30
4
A:21-30
B:20-30
C:20-30
D:20-30
10
11
11
11
1.3
ENST00000367028
3
ENSE00000792110
chr1:
209879156-209879286
131
DHI1_HUMAN
30-73
44
4
A:30-73
B:30-73
C:30-73
D:30-73
44
44
44
44
1.4
ENST00000367028
4
ENSE00000792111
chr1:
209880054-209880165
112
DHI1_HUMAN
74-111
38
4
A:74-111
B:74-111
C:74-111
D:74-111
38
38
38
38
1.5
ENST00000367028
5
ENSE00000792112
chr1:
209880288-209880473
186
DHI1_HUMAN
111-173
63
4
A:111-173
B:111-173
C:111-173
D:111-173
63
63
63
63
1.6
ENST00000367028
6
ENSE00000792113
chr1:
209905781-209905924
144
DHI1_HUMAN
173-221
49
4
A:173-221
B:173-221
C:173-221
D:173-221
49
49
49
49
1.7a
ENST00000367028
7a
ENSE00001443286
chr1:
209907649-209908209
561
DHI1_HUMAN
221-292
72
4
A:221-282 (gaps)
B:221-284
C:221-281 (gaps)
D:221-281 (gaps)
62
64
61
61
[
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3d4na_ (A:)
1b: SCOP_d3d4nb_ (B:)
1c: SCOP_d3d4nc_ (C:)
1d: SCOP_d3d4nd_ (D:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Tyrosine-dependent oxidoreductases
(503)
Protein domain
:
11-beta-hydroxysteroid dehydrogenase 1
(34)
Human (Homo sapiens) [TaxId: 9606]
(25)
1a
d3d4na_
A:
1b
d3d4nb_
B:
1c
d3d4nc_
C:
1d
d3d4nd_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3d4nC00 (C:20-281)
1b: CATH_3d4nA00 (A:21-282)
1c: CATH_3d4nD00 (D:20-281)
1d: CATH_3d4nB00 (B:20-284)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
3d4nC00
C:20-281
1b
3d4nA00
A:21-282
1c
3d4nD00
D:20-281
1d
3d4nB00
B:20-284
[
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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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