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5K32
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (120 KB)
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(1)
Title
:
PDE4D CRYSTAL STRUCTURE IN COMPLEX WITH SMALL MOLECULE INHIBITOR
Authors
:
V. Segarra, B. Hernandez, R. Roberts, J. Gracia, M. Soler, I. Bonin, J. A
Date
:
19 May 16 (Deposition) - 29 Mar 17 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.99
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Phosphodiesterases, Inhibitor, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. S. Roberts, S. Sevilla, M. Ferrer, J. Taltavull, B. Hernandez, J. Gracia, V. Segarra, M. D. Lehner, A. Gavalda, M. Andres, J. Cabedo, D. Vilella, E. Calama, C. Carcasona, M. Miralpeix, M. Martinell, J. Aymami
4-Amino-7, 8-Dihydro-1, 6-Naphthyridin-5(6H)-Ones As Inhaled Pde4 Inhibitors: Structural Biology, Structure-Activity Relationships And Binding Kinetics
To Be Published
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close entry info
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Hetero Components
(4, 38)
Info
All Hetero Components
1a: 4-[(3-METHOXYPHENYL)AMINO]-2-PHENY... (6Q2a)
1b: 4-[(3-METHOXYPHENYL)AMINO]-2-PHENY... (6Q2b)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2ae: 1,2-ETHANEDIOL (EDOae)
2af: 1,2-ETHANEDIOL (EDOaf)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6Q2
2
Ligand/Ion
4-[(3-METHOXYPHENYL)AMINO]-2-PHENYL-7,8-DIHYDRO-1,6-NAPHTHYRIDIN-5(6H)-ONE
2
EDO
32
Ligand/Ion
1,2-ETHANEDIOL
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
ZN
2
Ligand/Ion
ZINC ION
[
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Sites
(37, 37)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
35: AF8 (SOFTWARE)
36: AF9 (SOFTWARE)
37: AG1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , MG A:1002 , HOH A:1154 , HOH A:1214
binding site for residue ZN A 1001
02
AC2
SOFTWARE
ASP A:201 , ZN A:1001 , HOH A:1141 , HOH A:1169 , HOH A:1200 , HOH A:1214 , HOH A:1218
binding site for residue MG A 1002
03
AC3
SOFTWARE
TYR A:159 , THR A:271 , MET A:273 , ASP A:318 , ASN A:321 , THR A:333 , GLN A:369 , PHE A:372 , EDO A:1010 , EDO A:1011 , EDO A:1013 , HOH A:1122 , HOH A:1186
binding site for residue 6Q2 A 1003
04
AC4
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH A:1108 , ASN B:224
binding site for residue EDO A 1004
05
AC5
SOFTWARE
ASN A:209 , GLN A:210 , HOH A:1107 , HOH A:1133 , HOH A:1162 , HOH A:1182
binding site for residue EDO A 1005
06
AC6
SOFTWARE
GLU A:150 , TYR A:153 , ASN A:162 , EDO A:1007 , HOH A:1125 , HOH A:1151 , HOH A:1314 , GLN B:407
binding site for residue EDO A 1006
07
AC7
SOFTWARE
ASN A:115 , ALA A:155 , ASN A:161 , ASN A:162 , ILE A:163 , EDO A:1006 , HOH A:1151
binding site for residue EDO A 1007
08
AC8
SOFTWARE
VAL A:174 , SER A:177 , THR A:178 , ASP A:391 , HOH A:1112
binding site for residue EDO A 1008
09
AC9
SOFTWARE
PHE A:238 , ARG A:257 , HOH A:1193
binding site for residue EDO A 1009
10
AD1
SOFTWARE
HIS A:204 , GLY A:206 , VAL A:207 , SER A:208 , GLU A:339 , PHE A:340 , GLN A:343 , 6Q2 A:1003 , HOH A:1126 , HOH A:1252
binding site for residue EDO A 1010
11
AD2
SOFTWARE
SER A:368 , GLY A:371 , PHE A:372 , 6Q2 A:1003
binding site for residue EDO A 1011
12
AD3
SOFTWARE
HIS A:154 , ASP A:203 , PRO A:205 , LEU A:219
binding site for residue EDO A 1012
13
AD4
SOFTWARE
MET A:273 , 6Q2 A:1003
binding site for residue EDO A 1013
14
AD5
SOFTWARE
ALA A:183 , VAL A:184 , HOH A:1103 , GLY B:114 , ASN B:115 , ARG B:116
binding site for residue EDO A 1014
15
AD6
SOFTWARE
PRO A:179 , ALA A:180 , SER A:295 , GLY A:296 , HIS A:389 , PRO A:390 , ASP A:391
binding site for residue EDO A 1015
16
AD7
SOFTWARE
LEU A:299 , ARG B:335 , ARG B:342 , HOH B:1113 , HOH B:1221
binding site for residue EDO A 1016
17
AD8
SOFTWARE
GLU A:366 , TRP A:405 , TYR A:406 , THR A:409
binding site for residue EDO A 1017
18
AD9
SOFTWARE
GLU A:111 , ARG A:335 , HOH A:1240
binding site for residue EDO A 1018
19
AE1
SOFTWARE
LYS A:275 , HOH A:1188
binding site for residue EDO A 1019
20
AE2
SOFTWARE
HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , MG B:1002 , HOH B:1150 , HOH B:1186
binding site for residue ZN B 1001
21
AE3
SOFTWARE
ASP B:201 , ZN B:1001 , HOH B:1147 , HOH B:1150 , HOH B:1162 , HOH B:1178 , HOH B:1238
binding site for residue MG B 1002
22
AE4
SOFTWARE
TYR B:159 , MET B:273 , ASP B:318 , ASN B:321 , TRP B:332 , THR B:333 , ILE B:336 , PHE B:340 , GLN B:369 , PHE B:372 , EDO B:1012 , EDO B:1013 , HOH B:1128
binding site for residue 6Q2 B 1003
23
AE5
SOFTWARE
PRO A:411 , GLU B:366 , TRP B:405 , TYR B:406 , HOH B:1127
binding site for residue EDO B 1004
24
AE6
SOFTWARE
PHE B:238 , ARG B:257 , ARG B:261 , EDO B:1006 , HOH B:1119 , HOH B:1196
binding site for residue EDO B 1005
25
AE7
SOFTWARE
ARG B:257 , GLN B:258 , EDO B:1005 , HOH B:1212
binding site for residue EDO B 1006
26
AE8
SOFTWARE
LYS B:262 , ASP B:266 , HOH B:1102 , HOH B:1203
binding site for residue EDO B 1007
27
AE9
SOFTWARE
TRP A:405 , ASP B:401 , ASN B:402
binding site for residue EDO B 1008
28
AF1
SOFTWARE
MET B:277 , LYS B:284
binding site for residue EDO B 1009
29
AF2
SOFTWARE
ASP A:151 , HIS A:152 , GLY B:371 , ASP B:374 , TYR B:375 , HOH B:1138
binding site for residue EDO B 1010
30
AF3
SOFTWARE
HIS B:160 , HIS B:204 , GLY B:206 , VAL B:207 , GLU B:339 , PHE B:340 , GLN B:343 , HOH B:1124 , HOH B:1143
binding site for residue EDO B 1011
31
AF4
SOFTWARE
SER B:368 , GLY B:371 , PHE B:372 , 6Q2 B:1003
binding site for residue EDO B 1012
32
AF5
SOFTWARE
MET B:273 , 6Q2 B:1003
binding site for residue EDO B 1013
33
AF6
SOFTWARE
LYS B:239
binding site for residue EDO B 1014
34
AF7
SOFTWARE
HIS B:154 , ASP B:203 , PRO B:205 , LEU B:219
binding site for residue EDO B 1015
35
AF8
SOFTWARE
THR B:293 , SER B:294 , VAL B:297 , HOH B:1303
binding site for residue EDO B 1016
36
AF9
SOFTWARE
VAL A:297 , LEU A:299 , HOH B:1142
binding site for residue EDO B 1018
37
AG1
SOFTWARE
ALA B:183 , PHE B:185 , ILE B:190 , HOH B:1116
binding site for residue EDO B 1019
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
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SCOP Domains
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CATH Domains
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Sorry, no Info available
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Pfam Domains
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Sorry, no Info available
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