PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4AJL
Asym. Unit
Info
Asym.Unit (443 KB)
Biol.Unit 1 (436 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
RAT LDHA IN COMPLEX WITH 3-(ETHYLCARBAMOYLAMINO)-N-(2-METHYL-1,3-BENZOTHIAZOL-6-YL)PROPANAMIDE
Authors
:
J. A. Tucker, C. Brassington, G. Hassall, M. Vogtherr, R. Ward, J. Tart, M. Addie, A. Ferguson
Date
:
16 Feb 12 (Deposition) - 21 Mar 12 (Release) - 25 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase-Inhibitor Complex, Fragment Based Lead Generated Inhibitors
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Ward, C. Brassington, A. L. Breeze, A. Caputo, S. Critchlow, G. Davies, L. Goodwin, G. Hassall, R. Greenwood, G. Holdgate, M. Mrosek, R. A. Norman, S. Pearson, J. Tart, J. A. Tucker, M. Vogtherr, D. Whittaker, J. Wingfield, J. Winter, K. Hudson
The Design And Synthesis Of Novel Lactate Dehydrogenase A Inhibitors By Fragment-Based Lead Generation
J. Med. Chem. V. 55 3285 2012
[
close entry info
]
Hetero Components
(4, 19)
Info
All Hetero Components
1a: N~3~-(ETHYLCARBAMOYL)-N-(2-METHYL-... (88Wa)
1b: N~3~-(ETHYLCARBAMOYL)-N-(2-METHYL-... (88Wb)
1c: N~3~-(ETHYLCARBAMOYL)-N-(2-METHYL-... (88Wc)
1d: N~3~-(ETHYLCARBAMOYL)-N-(2-METHYL-... (88Wd)
2a: DIMETHYL SULFOXIDE (DMSa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
4a: MALONATE ION (MLIa)
4b: MALONATE ION (MLIb)
4c: MALONATE ION (MLIc)
4d: MALONATE ION (MLId)
4e: MALONATE ION (MLIe)
4f: MALONATE ION (MLIf)
4g: MALONATE ION (MLIg)
4h: MALONATE ION (MLIh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
88W
4
Ligand/Ion
N~3~-(ETHYLCARBAMOYL)-N-(2-METHYL-1,3-BENZOTHIAZOL-6-YL)-BETA-ALANINAMIDE
2
DMS
1
Ligand/Ion
DIMETHYL SULFOXIDE
3
GOL
6
Ligand/Ion
GLYCEROL
4
MLI
8
Ligand/Ion
MALONATE ION
[
close Hetero Component info
]
Sites
(19, 19)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN C:163 , SER C:166 , ALA C:167 , ARG C:170 , VAL C:269 , HIS C:270 , PRO C:271 , MLI C:1338 , HOH C:2189 , HOH C:2236 , HOH C:2246 , LEU D:69
BINDING SITE FOR RESIDUE GOL C1332
02
AC2
SOFTWARE
SER B:201 , GLY B:202 , ASN B:204 , GLY B:207 , SER C:201 , GLY C:202 , GLY C:207 , SER C:209
BINDING SITE FOR RESIDUE GOL C1334
03
AC3
SOFTWARE
MET A:40 , HOH A:2048 , MET B:40 , ASP B:42 , PHE B:70 , LEU B:71 , HOH B:2092
BINDING SITE FOR RESIDUE GOL B1332
04
AC4
SOFTWARE
LYS C:41 , MET D:40 , ASP D:42 , HOH D:2034 , HOH D:2061
BINDING SITE FOR RESIDUE GOL D1332
05
AC5
SOFTWARE
SER A:201 , GLY A:202 , ASN A:204 , GLY A:207 , SER A:209 , GLY D:202 , ASN D:204 , GLY D:207
BINDING SITE FOR RESIDUE GOL A1332
06
AC6
SOFTWARE
SER C:104 , ASN C:107 , HOH C:2274 , HOH C:2276
BINDING SITE FOR RESIDUE GOL C1335
07
AC7
SOFTWARE
GLY C:96 , ALA C:97 , 88W C:1336 , HOH C:2272 , HOH C:2273
BINDING SITE FOR RESIDUE DMS C1333
08
AC8
SOFTWARE
GLY A:26 , GLY A:28 , ASP A:51 , VAL A:52 , THR A:94 , ALA A:95 , GLY A:96 , PHE A:118 , ILE A:119 , HOH A:2031 , HOH A:2035 , HOH A:2124
BINDING SITE FOR RESIDUE 88W A1333
09
AC9
SOFTWARE
ASP B:51 , VAL B:52 , THR B:94 , ALA B:95 , GLY B:96 , ARG B:98 , ILE B:119 , HOH B:2032 , HOH B:2036 , HOH B:2106
BINDING SITE FOR RESIDUE 88W B1333
10
BC1
SOFTWARE
GLY C:28 , ASP C:51 , VAL C:52 , THR C:94 , ALA C:95 , GLY C:96 , PHE C:118 , ILE C:119 , DMS C:1333 , HOH C:2018 , HOH C:2022 , HOH C:2045 , HOH C:2093
BINDING SITE FOR RESIDUE 88W C1336
11
BC2
SOFTWARE
GLY D:28 , ASP D:51 , VAL D:52 , THR D:94 , ALA D:95 , GLY D:96 , ILE D:119 , HOH D:2020 , HOH D:2024 , HOH D:2076
BINDING SITE FOR RESIDUE 88W D1333
12
BC3
SOFTWARE
GLN C:99 , ARG C:105 , ASN C:137 , LEU C:164 , ARG C:168 , HIS C:192 , ALA C:237 , THR C:247
BINDING SITE FOR RESIDUE MLI C1337
13
BC4
SOFTWARE
ARG A:105 , ASN A:137 , LEU A:164 , ARG A:168 , HIS A:192 , ALA A:237 , THR A:247 , HOH A:2201 , HOH A:2302
BINDING SITE FOR RESIDUE MLI A1334
14
BC5
SOFTWARE
ARG B:170 , HIS B:185 , TRP B:187 , VAL B:269 , HOH B:2195 , HOH B:2210 , HOH B:2281 , HOH B:2325 , HOH B:2326 , SER C:183 , HIS C:185
BINDING SITE FOR RESIDUE MLI B1334
15
BC6
SOFTWARE
GLN B:99 , ARG B:105 , ASN B:137 , ARG B:168 , HIS B:192 , ALA B:237 , THR B:247
BINDING SITE FOR RESIDUE MLI B1335
16
BC7
SOFTWARE
ARG A:170 , HIS A:185 , VAL A:269 , HOH A:2230 , HOH A:2254 , HOH A:2327 , HOH A:2356 , HOH A:2357 , SER D:183 , HIS D:185
BINDING SITE FOR RESIDUE MLI A1335
17
BC8
SOFTWARE
SER B:183 , HIS B:185 , HOH B:2205 , HOH B:2206 , HOH B:2207 , ARG C:170 , HIS C:185 , VAL C:269 , GOL C:1332 , HOH C:2177 , HOH C:2243 , HOH C:2246
BINDING SITE FOR RESIDUE MLI C1338
18
BC9
SOFTWARE
ARG D:105 , ASN D:137 , LEU D:164 , ARG D:168 , HIS D:192 , ALA D:237 , THR D:247 , HOH D:2092 , HOH D:2120 , HOH D:2185
BINDING SITE FOR RESIDUE MLI D1334
19
CC1
SOFTWARE
SER A:183 , HIS A:185 , HOH A:2249 , HOH A:2250 , HOH A:2251 , ARG D:170 , HIS D:185 , VAL D:269 , HOH D:2144 , HOH D:2199
BINDING SITE FOR RESIDUE MLI D1335
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: L_LDH (A:189-195,B:189-195,C:189-195,D:18...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
L_LDH
PS00064
L-lactate dehydrogenase active site.
LDHA_RAT
190-196
4
A:189-195
B:189-195
C:189-195
D:189-195
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d4ajla2 (A:160-331)
1b: SCOP_d4ajlb2 (B:160-331)
1c: SCOP_d4ajlc2 (C:160-331)
1d: SCOP_d4ajld2 (D:160-331)
2a: SCOP_d4ajla1 (A:2-159)
2b: SCOP_d4ajlb1 (B:2-159)
2c: SCOP_d4ajlc1 (C:1-159)
2d: SCOP_d4ajld1 (D:1-159)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
Lactate & malate dehydrogenases, C-terminal domain
(125)
Protein domain
:
automated matches
(30)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(12)
1a
d4ajla2
A:160-331
1b
d4ajlb2
B:160-331
1c
d4ajlc2
C:160-331
1d
d4ajld2
D:160-331
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
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(12)
2a
d4ajla1
A:2-159
2b
d4ajlb1
B:2-159
2c
d4ajlc1
C:1-159
2d
d4ajld1
D:1-159
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (443 KB)
Header - Asym.Unit
Biol.Unit 1 (436 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4AJL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
