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.
4I9N
Asym. Unit
Info
Asym.Unit (428 KB)
Biol.Unit 1 (214 KB)
Biol.Unit 2 (214 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF RABBIT LDHA IN COMPLEX WITH AP28161 AND AP28122
Authors
:
T. Zhou, A. Kohlmann, Z. G. Stephan, F. Li, L. Commodore, M. T. Greenfiel W. C. Shakespeare, X. Zhu, D. C. Dalgarno
Date
:
05 Dec 12 (Deposition) - 23 Jan 13 (Release) - 27 Feb 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Cancer, Fragment, Inhibitor, Oxidoreductase-Oxidoreductase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Kohlmann, S. G. Zech, F. Li, T. Zhou, R. M. Squillace, L. Commodore, M. T. Greenfield, X. Lu, D. P. Miller, W. S. Huang, J. Qi, R. M. Thomas, Y. Wang, S. Zhang, R. Dodd, S. Liu, R. Xu, Y. Xu, J. J. Miret, V. Rivera, T. Clackson, W. C. Shakespeare, X. Zhu, D. C. Dalgarno
Fragment Growing And Linking Lead To Novel Nanomolar Lactat Dehydrogenase Inhibitors.
J. Med. Chem. V. 56 1023 2013
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: 6-[3-(CARBOXYMETHOXY)-5-FLUOROPHEN... (1E5a)
1b: 6-[3-(CARBOXYMETHOXY)-5-FLUOROPHEN... (1E5b)
1c: 6-[3-(CARBOXYMETHOXY)-5-FLUOROPHEN... (1E5c)
1d: 6-[3-(CARBOXYMETHOXY)-5-FLUOROPHEN... (1E5d)
1e: 6-[3-(CARBOXYMETHOXY)-5-FLUOROPHEN... (1E5e)
1f: 6-[3-(CARBOXYMETHOXY)-5-FLUOROPHEN... (1E5f)
1g: 6-[3-(CARBOXYMETHOXY)-5-FLUOROPHEN... (1E5g)
1h: 6-[3-(CARBOXYMETHOXY)-5-FLUOROPHEN... (1E5h)
2a: 6-({2-[(5-CHLORO-4-{[(2S)-2,3-DIHY... (1E6a)
2b: 6-({2-[(5-CHLORO-4-{[(2S)-2,3-DIHY... (1E6b)
2c: 6-({2-[(5-CHLORO-4-{[(2S)-2,3-DIHY... (1E6c)
2d: 6-({2-[(5-CHLORO-4-{[(2S)-2,3-DIHY... (1E6d)
2e: 6-({2-[(5-CHLORO-4-{[(2S)-2,3-DIHY... (1E6e)
2f: 6-({2-[(5-CHLORO-4-{[(2S)-2,3-DIHY... (1E6f)
2g: 6-({2-[(5-CHLORO-4-{[(2S)-2,3-DIHY... (1E6g)
2h: 6-({2-[(5-CHLORO-4-{[(2S)-2,3-DIHY... (1E6h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1E5
8
Ligand/Ion
6-[3-(CARBOXYMETHOXY)-5-FLUOROPHENYL]PYRIDINE-3-CARBOXYLIC ACID
2
1E6
8
Ligand/Ion
6-({2-[(5-CHLORO-4-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}-2-METHOXYPHENYL)AMINO]-2-OXOETHYL}SULFANYL)PYRIDINE-3-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:26 , GLY A:28 , ASP A:51 , VAL A:52 , THR A:94 , ALA A:95 , GLY A:96 , ILE A:115 , PHE A:118 , ILE A:119 , 1E5 A:402 , HOH A:517
BINDING SITE FOR RESIDUE 1E6 A 401
02
AC2
SOFTWARE
GLY A:28 , ALA A:29 , VAL A:30 , THR A:94 , VAL A:135 , SER A:136 , ASN A:137 , ARG A:168 , ALA A:237 , THR A:247 , 1E6 A:401 , HOH A:509 , HOH A:518 , HOH A:546
BINDING SITE FOR RESIDUE 1E5 A 402
03
AC3
SOFTWARE
GLY B:26 , GLY B:28 , ASP B:51 , VAL B:52 , THR B:94 , ALA B:95 , GLY B:96 , ARG B:111 , ILE B:115 , PHE B:118 , ILE B:119 , 1E5 B:402
BINDING SITE FOR RESIDUE 1E6 B 401
04
AC4
SOFTWARE
GLY B:28 , ALA B:29 , VAL B:30 , THR B:94 , VAL B:135 , SER B:136 , ASN B:137 , LEU B:164 , ARG B:168 , ALA B:237 , THR B:247 , 1E6 B:401 , HOH B:520 , HOH B:529 , HOH B:532
BINDING SITE FOR RESIDUE 1E5 B 402
05
AC5
SOFTWARE
GLY C:26 , GLY C:28 , ASP C:51 , VAL C:52 , THR C:94 , ALA C:95 , GLY C:96 , ARG C:111 , ILE C:115 , PHE C:118 , ILE C:119 , 1E5 C:402 , HOH C:534
BINDING SITE FOR RESIDUE 1E6 C 401
06
AC6
SOFTWARE
GLY C:28 , ALA C:29 , VAL C:30 , THR C:94 , VAL C:135 , SER C:136 , ASN C:137 , ARG C:168 , ALA C:237 , THR C:247 , 1E6 C:401 , HOH C:510 , HOH C:512
BINDING SITE FOR RESIDUE 1E5 C 402
07
AC7
SOFTWARE
GLY D:28 , ASP D:51 , VAL D:52 , THR D:94 , ALA D:95 , GLY D:96 , ARG D:111 , ASN D:114 , ILE D:115 , PHE D:118 , ILE D:119 , 1E5 D:402 , HOH D:535
BINDING SITE FOR RESIDUE 1E6 D 401
08
AC8
SOFTWARE
GLY D:28 , ALA D:29 , VAL D:30 , THR D:94 , VAL D:135 , SER D:136 , ASN D:137 , LEU D:164 , ARG D:168 , ALA D:237 , THR D:247 , 1E6 D:401 , HOH D:510 , HOH D:519
BINDING SITE FOR RESIDUE 1E5 D 402
09
AC9
SOFTWARE
GLY E:26 , GLY E:28 , ASP E:51 , VAL E:52 , THR E:94 , ALA E:95 , GLY E:96 , ARG E:98 , ARG E:111 , ASN E:114 , ILE E:115 , PHE E:118 , ILE E:119 , 1E5 E:402
BINDING SITE FOR RESIDUE 1E6 E 401
10
BC1
SOFTWARE
GLY E:28 , ALA E:29 , VAL E:30 , THR E:94 , VAL E:135 , SER E:136 , ASN E:137 , ARG E:168 , ALA E:237 , THR E:247 , 1E6 E:401 , HOH E:506 , HOH E:515
BINDING SITE FOR RESIDUE 1E5 E 402
11
BC2
SOFTWARE
GLY F:26 , VAL F:27 , GLY F:28 , ASP F:51 , VAL F:52 , THR F:94 , ALA F:95 , GLY F:96 , ARG F:98 , ARG F:111 , ASN F:114 , ILE F:115 , PHE F:118 , 1E5 F:402 , HOH F:508
BINDING SITE FOR RESIDUE 1E6 F 401
12
BC3
SOFTWARE
GLY F:28 , ALA F:29 , VAL F:30 , THR F:94 , VAL F:135 , SER F:136 , ASN F:137 , ARG F:168 , ALA F:237 , THR F:247 , 1E6 F:401 , HOH F:509
BINDING SITE FOR RESIDUE 1E5 F 402
13
BC4
SOFTWARE
VAL G:25 , GLY G:26 , GLY G:28 , ASP G:51 , VAL G:52 , THR G:94 , ALA G:95 , GLY G:96 , ARG G:111 , ILE G:115 , PHE G:118 , ILE G:119 , 1E5 G:402 , HOH G:522
BINDING SITE FOR RESIDUE 1E6 G 401
14
BC5
SOFTWARE
GLY G:28 , VAL G:30 , THR G:94 , VAL G:135 , SER G:136 , ASN G:137 , LEU G:164 , ARG G:168 , ALA G:237 , THR G:247 , 1E6 G:401 , HOH G:511 , HOH G:539
BINDING SITE FOR RESIDUE 1E5 G 402
15
BC6
SOFTWARE
GLY H:26 , GLY H:28 , ASP H:51 , VAL H:52 , THR H:94 , ALA H:95 , GLY H:96 , ARG H:111 , ILE H:115 , PHE H:118 , ILE H:119 , 1E5 H:402
BINDING SITE FOR RESIDUE 1E6 H 401
16
BC7
SOFTWARE
GLY H:28 , ALA H:29 , VAL H:30 , THR H:94 , VAL H:135 , SER H:136 , ASN H:137 , ARG H:168 , ALA H:237 , THR H:247 , 1E6 H:401 , HOH H:513 , HOH H:527
BINDING SITE FOR RESIDUE 1E5 H 402
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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, 16)
Info
All SCOP Domains
1a: SCOP_d4i9na2 (A:160-331)
1b: SCOP_d4i9nb2 (B:160-331)
1c: SCOP_d4i9nc2 (C:160-331)
1d: SCOP_d4i9nd2 (D:160-331)
1e: SCOP_d4i9ne2 (E:160-331)
1f: SCOP_d4i9nf2 (F:160-331)
1g: SCOP_d4i9ng2 (G:160-331)
1h: SCOP_d4i9nh2 (H:160-331)
2a: SCOP_d4i9na1 (A:1-159)
2b: SCOP_d4i9nb1 (B:1-159)
2c: SCOP_d4i9nc1 (C:1-159)
2d: SCOP_d4i9nd1 (D:1-159)
2e: SCOP_d4i9ne1 (E:1-159)
2f: SCOP_d4i9nf1 (F:1-159)
2g: SCOP_d4i9ng1 (G:1-159)
2h: SCOP_d4i9nh1 (H: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)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(5)
1a
d4i9na2
A:160-331
1b
d4i9nb2
B:160-331
1c
d4i9nc2
C:160-331
1d
d4i9nd2
D:160-331
1e
d4i9ne2
E:160-331
1f
d4i9nf2
F:160-331
1g
d4i9ng2
G:160-331
1h
d4i9nh2
H: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
:
LDH N-terminal domain-like
(117)
Protein domain
:
automated matches
(15)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(5)
2a
d4i9na1
A:1-159
2b
d4i9nb1
B:1-159
2c
d4i9nc1
C:1-159
2d
d4i9nd1
D:1-159
2e
d4i9ne1
E:1-159
2f
d4i9nf1
F:1-159
2g
d4i9ng1
G:1-159
2h
d4i9nh1
H: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
Chain E
Chain F
Chain G
Chain H
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 (428 KB)
Header - Asym.Unit
Biol.Unit 1 (214 KB)
Header - Biol.Unit 1
Biol.Unit 2 (214 KB)
Header - Biol.Unit 2
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
4I9N
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
