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4AJP
Asym. Unit
Info
Asym.Unit (428 KB)
Biol.Unit 1 (420 KB)
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(1)
Title
:
HUMAN LDHA IN COMPLEX WITH 2-((4-(4-((3-((2-METHYL-1,3-BENZOTHIAZOL-6YL)AMINO)-3-OXO-PROPYL)AMINO)-4-OXO-BUTYL) PHENYL)METHYL)PROPANEDIOIC ACID
Authors
:
J. A. Tucker, C. Brassington, A. Caputo, R. Ward, S. Pearson, M. Watson, G. Davies
Date
:
16 Feb 12 (Deposition) - 21 Mar 12 (Release) - 17 Sep 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.38
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
[
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Hetero Components
(3, 18)
Info
All Hetero Components
1a: {4-[4-({3-[(2-METHYL-1,3-BENZOTHIA... (88Na)
1b: {4-[4-({3-[(2-METHYL-1,3-BENZOTHIA... (88Nb)
1c: {4-[4-({3-[(2-METHYL-1,3-BENZOTHIA... (88Nc)
1d: {4-[4-({3-[(2-METHYL-1,3-BENZOTHIA... (88Nd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
88N
4
Ligand/Ion
{4-[4-({3-[(2-METHYL-1,3-BENZOTHIAZOL-6-YL)AMINO]-3-OXOPROPYL}AMINO)-4-OXOBUTYL]BENZYL}PROPANEDIOIC ACID
2
GOL
3
Ligand/Ion
GLYCEROL
3
SO4
11
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:201 , GLY A:202 , ASN A:204 , GLY A:207 , SER C:201 , GLY C:202 , ASN C:204 , GLY C:207 , SER C:209
BINDING SITE FOR RESIDUE GOL C1332
02
AC2
SOFTWARE
ALA B:29 , ARG B:98 , HOH B:2007 , HOH B:2108
BINDING SITE FOR RESIDUE GOL B1332
03
AC3
SOFTWARE
PRO C:153 , ASN C:155 , ARG C:156
BINDING SITE FOR RESIDUE GOL C1333
04
AC4
SOFTWARE
GLY A:28 , VAL A:30 , ASP A:51 , VAL A:52 , THR A:94 , ALA A:95 , GLY A:96 , GLN A:99 , ARG A:105 , VAL A:135 , ASN A:137 , ARG A:168 , HIS A:192 , ALA A:237 , THR A:247 , HOH A:2011 , HOH A:2014 , HOH A:2042
BINDING SITE FOR RESIDUE 88N A1332
05
AC5
SOFTWARE
GLY B:28 , VAL B:30 , ASP B:51 , VAL B:52 , THR B:94 , ALA B:95 , GLY B:96 , GLN B:99 , ARG B:105 , VAL B:135 , ASN B:137 , LEU B:164 , ARG B:168 , HIS B:192 , ALA B:237 , THR B:247 , HOH B:2005 , HOH B:2007 , HOH B:2029 , HOH B:2039
BINDING SITE FOR RESIDUE 88N B1333
06
AC6
SOFTWARE
VAL C:30 , ASP C:51 , VAL C:52 , THR C:94 , ALA C:95 , GLY C:96 , GLN C:99 , ARG C:105 , PHE C:118 , VAL C:135 , ASN C:137 , ARG C:168 , HIS C:192 , ALA C:237 , THR C:247 , HOH C:2004 , HOH C:2005 , HOH C:2033
BINDING SITE FOR RESIDUE 88N C1334
07
AC7
SOFTWARE
GLY D:26 , VAL D:30 , ASP D:51 , VAL D:52 , THR D:94 , ALA D:95 , GLY D:96 , GLN D:99 , ARG D:105 , VAL D:135 , ASN D:137 , LEU D:164 , ARG D:168 , HIS D:192 , ALA D:237 , THR D:247 , HOH D:2005 , HOH D:2008 , HOH D:2023 , HOH D:2026
BINDING SITE FOR RESIDUE 88N D1332
08
AC8
SOFTWARE
ARG B:170 , HIS B:185 , HOH B:2063 , HOH B:2070 , HOH B:2099 , HOH B:2109 , HIS D:185
BINDING SITE FOR RESIDUE SO4 B1334
09
AC9
SOFTWARE
HIS B:185 , HOH B:2069 , HOH B:2083 , ARG D:170 , HIS D:185 , TRP D:187 , HOH D:2051
BINDING SITE FOR RESIDUE SO4 D1333
10
BC1
SOFTWARE
SER A:183 , HIS A:185 , HOH A:2083 , HOH A:2094 , ARG C:170 , HIS C:185 , HOH C:2061
BINDING SITE FOR RESIDUE SO4 C1335
11
BC2
SOFTWARE
ARG A:170 , HIS A:185 , HOH A:2078 , HOH A:2085 , HOH A:2121 , HIS C:185
BINDING SITE FOR RESIDUE SO4 A1333
12
BC3
SOFTWARE
TRP A:147 , PRO A:153 , LYS A:154
BINDING SITE FOR RESIDUE SO4 A1334
13
BC4
SOFTWARE
TRP B:147 , PHE B:152 , PRO B:153 , LYS B:154 , HOH B:2057
BINDING SITE FOR RESIDUE SO4 B1335
14
BC5
SOFTWARE
LYS A:148 , HOH A:2065 , ASN B:83 , TYR B:126
BINDING SITE FOR RESIDUE SO4 A1335
15
BC6
SOFTWARE
ASN A:83 , TYR A:126 , LYS B:148
BINDING SITE FOR RESIDUE SO4 A1336
16
BC7
SOFTWARE
TRP C:147 , PHE C:152 , PRO C:153 , LYS C:154
BINDING SITE FOR RESIDUE SO4 C1336
17
BC8
SOFTWARE
THR A:308 , SER A:309 , THR B:219 , ASP B:220
BINDING SITE FOR RESIDUE SO4 B1336
18
BC9
SOFTWARE
TRP D:147 , PHE D:152 , PRO D:153 , LYS D:154
BINDING SITE FOR RESIDUE SO4 D1334
[
close Site info
]
SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_059374 (S160R, chain A/B/C/D, )
2: VAR_004180 (K221E, chain A/B/C/D, )
3: VAR_004181 (R314C, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_059374
S
161
R
LDHA_HUMAN
Polymorphism
5030621
A/B/C/D
S
160
R
2
UniProt
VAR_004180
K
222
E
LDHA_HUMAN
Polymorphism
---
A/B/C/D
K
221
E
3
UniProt
VAR_004181
R
315
C
LDHA_HUMAN
Polymorphism
---
A/B/C/D
R
314
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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_HUMAN
190-196
4
A:189-195
B:189-195
C:189-195
D:189-195
[
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Exons
(12, 48)
Info
All Exons
Exon 1.3a (A:1-41 (gaps) | B:1-41 (gaps) | C:...)
Exon 1.5b (A:42-81 | B:42-81 | C:42-81 | D:42...)
Exon 1.6c (A:81-139 | B:81-139 | C:81-139 | D...)
Exon 1.7 (A:139-197 | B:139-197 | C:139-197 ...)
Exon 1.8c (A:197-231 | B:197-231 | C:197-231 ...)
Exon 1.9 (A:231-232 | B:231-232 | C:231-232 ...)
Exon 1.10 (A:232-250 | B:232-250 | C:232-250 ...)
Exon 1.11 (A:250-253 | B:250-253 | C:250-253 ...)
Exon 1.12 (A:253-262 | B:253-262 | C:253-262 ...)
Exon 1.13 (A:262-271 | B:262-271 | C:262-271 ...)
Exon 1.14b (A:271-276 | B:271-276 | C:271-276 ...)
Exon 1.15a (A:277-330 | B:277-330 | C:277-330 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1f/1.3a
02: Boundary 1.3a/1.5b
03: Boundary 1.5b/1.6c
04: Boundary 1.6c/1.7
05: Boundary 1.7/1.8c
06: Boundary 1.8c/1.9
07: Boundary 1.9/1.10
08: Boundary 1.10/1.11
09: Boundary 1.11/1.12
10: Boundary 1.12/1.13
11: Boundary 1.13/1.14b
12: Boundary 1.14b/1.15a
13: Boundary 1.15a/-
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
1.1f
ENST00000379412
1f
ENSE00001524368
chr11:
18416112-18416183
72
LDHA_HUMAN
-
0
0
-
-
1.3a
ENST00000379412
3a
ENSE00002196319
chr11:
18418366-18418515
150
LDHA_HUMAN
1-42
42
4
A:1-41 (gaps)
B:1-41 (gaps)
C:1-41 (gaps)
D:1-41
41
41
41
41
1.5b
ENST00000379412
5b
ENSE00000886595
chr11:
18420978-18421095
118
LDHA_HUMAN
43-82
40
4
A:42-81
B:42-81
C:42-81
D:42-81
40
40
40
40
1.6c
ENST00000379412
6c
ENSE00001106716
chr11:
18422384-18422557
174
LDHA_HUMAN
82-140
59
4
A:81-139
B:81-139
C:81-139
D:81-139
59
59
59
59
1.7
ENST00000379412
7
ENSE00001639138
chr11:
18424387-18424560
174
LDHA_HUMAN
140-198
59
4
A:139-197
B:139-197
C:139-197
D:139-197
59
59
59
59
1.8c
ENST00000379412
8c
ENSE00001655143
chr11:
18425241-18425343
103
LDHA_HUMAN
198-232
35
4
A:197-231
B:197-231
C:197-231
D:197-231
35
35
35
35
1.9
ENST00000379412
9
ENSE00001610496
chr11:
18425416-18425418
3
LDHA_HUMAN
232-233
2
4
A:231-232
B:231-232
C:231-232
D:231-232
2
2
2
2
1.10
ENST00000379412
10
ENSE00001721839
chr11:
18426327-18426380
54
LDHA_HUMAN
233-251
19
4
A:232-250
B:232-250
C:232-250
D:232-250
19
19
19
19
1.11
ENST00000379412
11
ENSE00001697756
chr11:
18426430-18426437
8
LDHA_HUMAN
251-254
4
4
A:250-253
B:250-253
C:250-253
D:250-253
4
4
4
4
1.12
ENST00000379412
12
ENSE00001605016
chr11:
18426514-18426540
27
LDHA_HUMAN
254-263
10
4
A:253-262
B:253-262
C:253-262
D:253-262
10
10
10
10
1.13
ENST00000379412
13
ENSE00001770181
chr11:
18426715-18426741
27
LDHA_HUMAN
263-272
10
4
A:262-271
B:262-271
C:262-271
D:262-271
10
10
10
10
1.14b
ENST00000379412
14b
ENSE00001654863
chr11:
18427103-18427119
17
LDHA_HUMAN
272-277
6
4
A:271-276
B:271-276
C:271-276
D:271-276
6
6
6
6
1.15a
ENST00000379412
15a
ENSE00001681791
chr11:
18428664-18429393
730
LDHA_HUMAN
278-331
54
4
A:277-330
B:277-330
C:277-330
D:277-330
54
54
54
54
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d4ajpa2 (A:160-331)
1b: SCOP_d4ajpb2 (B:160-331)
1c: SCOP_d4ajpc2 (C:160-331)
1d: SCOP_d4ajpd2 (D:160-331)
2a: SCOP_d4ajpa1 (A:1-159)
2b: SCOP_d4ajpb1 (B:1-159)
2c: SCOP_d4ajpc1 (C:1-159)
2d: SCOP_d4ajpd1 (D:1-159)
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Protein Domains
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(
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Organisms
(
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(
)
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)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d4ajpa2
A:160-331
1b
d4ajpb2
B:160-331
1c
d4ajpc2
C:160-331
1d
d4ajpd2
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)
Human (Homo sapiens) [TaxId: 9606]
(32)
2a
d4ajpa1
A:1-159
2b
d4ajpb1
B:1-159
2c
d4ajpc1
C:1-159
2d
d4ajpd1
D:1-159
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (428 KB)
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