Receptor
PDB id Resolution Class Description Source Keywords
4P3Y 2.15 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ACINETOBACTER BAUMANNII DSBA IN COMPLEX TU ESCHERICHIA COLI THIOREDOXIN RELATED DISULFIDE OXIDASE DSBA MULTIDRUG RESISDISULFIDE BOND FORMATION ANTI-BIOFILM FORMATION ANTIVIRULBACTERIAL INFECTION TRANSLATION-OXIDOREDUCTASE COMPLEX
Ref.: STRUCTURE OF THE ACINETOBACTER BAUMANNII DITHIOL OX DSBA BOUND TO ELONGATION FACTOR EF-TU REVEALS A NOV PROTEIN INTERACTION SITE. J.BIOL.CHEM. V. 289 19869 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:401;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
GOL A:403;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
GDP A:402;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4P3Y 2.15 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ACINETOBACTER BAUMANNII DSBA IN COMPLEX TU ESCHERICHIA COLI THIOREDOXIN RELATED DISULFIDE OXIDASE DSBA MULTIDRUG RESISDISULFIDE BOND FORMATION ANTI-BIOFILM FORMATION ANTIVIRULBACTERIAL INFECTION TRANSLATION-OXIDOREDUCTASE COMPLEX
Ref.: STRUCTURE OF THE ACINETOBACTER BAUMANNII DITHIOL OX DSBA BOUND TO ELONGATION FACTOR EF-TU REVEALS A NOV PROTEIN INTERACTION SITE. J.BIOL.CHEM. V. 289 19869 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4P3Y - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4P3Y - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 4P3Y - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 161
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 9GM 0.839506 0.973684
6 GNP 0.839506 0.973684
7 G 0.828947 0.986486
8 5GP 0.828947 0.986486
9 G1R 0.82716 0.986667
10 GCP 0.82716 0.973684
11 GSP 0.817073 0.948718
12 GAV 0.797619 0.961039
13 GMV 0.792683 0.973684
14 G2P 0.77381 0.961039
15 G2R 0.770115 0.961039
16 GP2 0.756098 0.961039
17 GDC 0.747253 0.961039
18 GKE 0.747253 0.961039
19 GDD 0.747253 0.961039
20 GPG 0.741573 0.961039
21 G3D 0.732558 0.986486
22 ALF 5GP 0.729412 0.888889
23 Y9Z 0.728261 0.902439
24 G5P 0.723404 0.973684
25 GFB 0.72043 0.961039
26 GTG 0.72043 0.936709
27 GDR 0.72043 0.961039
28 G4P 0.715909 0.986486
29 G3A 0.712766 0.973684
30 6CK 0.712766 0.936709
31 GDP AF3 0.7 0.888889
32 ALF GDP 0.7 0.888889
33 GDP ALF 0.7 0.888889
34 YGP 0.698925 0.901235
35 GKD 0.697917 0.961039
36 JB2 0.697917 0.961039
37 GDX 0.690722 0.973684
38 GPD 0.690722 0.925
39 GMP 0.684211 0.88
40 0O2 0.666667 0.986486
41 JB3 0.656863 0.948718
42 NGD 0.650485 0.961039
43 DGI 0.636364 0.923077
44 GDP 7MG 0.636364 0.911392
45 U2G 0.634615 0.936709
46 GPX 0.634409 0.946667
47 G G 0.632653 0.948052
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 CG2 0.622642 0.936709
52 FEG 0.619048 0.879518
53 MGD 0.614679 0.891566
54 ZGP 0.613208 0.869048
55 GH3 0.612903 0.973333
56 3GP 0.611765 0.946667
57 MD1 0.607143 0.891566
58 PGD 0.59292 0.925
59 DGT 0.591398 0.923077
60 BGO 0.588785 0.924051
61 TPG 0.582609 0.840909
62 DBG 0.582609 0.948718
63 2GP 0.574713 0.96
64 FE9 0.570175 0.776596
65 GCP G 0.56 0.921053
66 A G 0.553571 0.935065
67 G A A A 0.553571 0.923077
68 MGP 0.553191 0.961039
69 U A G G 0.548673 0.935065
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 G1R G1R 0.542373 0.924051
73 P2G 0.527473 0.883117
74 PGD O 0.525 0.850575
75 ADP 0.522222 0.92
76 R5I 0.520833 0.946667
77 R7I 0.520833 0.946667
78 GGM 0.517544 0.901235
79 DGP 0.516484 0.910256
80 DG 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G U 0.513274 0.9
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 AKW 0.504425 0.890244
86 G C 0.504348 0.9
87 GPC 0.491525 0.879518
88 G7M 0.483871 0.948052
89 6AD 0.479592 0.841463
90 ATP 0.473684 0.92
91 HEJ 0.473684 0.92
92 G2Q 0.471154 0.961039
93 5FA 0.46875 0.92
94 AQP 0.46875 0.92
95 GTA 0.468468 0.936709
96 7DD 0.468085 0.906667
97 G G G RPC 0.466102 0.875
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 B4P 0.457447 0.894737
102 AP5 0.457447 0.894737
103 A2D 0.456522 0.894737
104 6YZ 0.455446 0.896104
105 G G G C 0.455285 0.9125
106 5GP 5GP 0.454545 0.883117
107 ANP 0.454545 0.896104
108 ACQ 0.454545 0.896104
109 AT4 0.452632 0.884615
110 A G C C 0.451613 0.911392
111 APC G U 0.45082 0.886076
112 PRT 0.449541 0.959459
113 G U34 0.449153 0.888889
114 DG DG 0.448598 0.865854
115 ITT 0.447917 0.868421
116 BA3 0.446809 0.894737
117 C2E 0.444444 0.921053
118 PCG 0.444444 0.933333
119 35G 0.444444 0.933333
120 MGO 0.441176 0.864198
121 AN2 0.4375 0.907895
122 G C C C 0.4375 0.924051
123 M33 0.43299 0.883117
124 UCG 0.429688 0.911392
125 A G U 0.42963 0.888889
126 ACP 0.428571 0.896104
127 MGQ 0.424528 0.935897
128 AR6 0.424242 0.894737
129 7DT 0.424242 0.906667
130 APR 0.424242 0.894737
131 93A 0.42268 0.833333
132 A4P 0.420168 0.869048
133 G8D 0.42 0.875
134 AD9 0.42 0.896104
135 SAP 0.42 0.873418
136 AGS 0.42 0.873418
137 CA0 0.418367 0.896104
138 ATF 0.417476 0.884615
139 AGO 0.414634 0.888889
140 A G U U 0.414286 0.888889
141 NIA 0.413043 0.82716
142 MGV 0.412844 0.890244
143 TAT 0.411765 0.884615
144 T99 0.411765 0.884615
145 ADQ 0.411215 0.871795
146 A1R 0.411215 0.839506
147 RGT 0.410714 0.909091
148 CGP 0.409836 0.86747
149 C1Z 0.409091 0.986486
150 A 0.408602 0.893333
151 AMP 0.408602 0.893333
152 UP5 0.40678 0.873418
153 AMZ 0.406593 0.918919
154 C2R 0.406593 0.906667
155 JBT 0.405882 0.778947
156 A22 0.40566 0.907895
157 25L 0.405405 0.907895
158 ADX 0.40404 0.809524
159 8OD 0.401961 0.946667
160 50T 0.4 0.883117
161 4TC 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4P3Y; Ligand: GDP; Similar sites found with APoc: 145
This union binding pocket(no: 1) in the query (biounit: 4p3y.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z0F GDP 1.67598
2 1TAD GDP 3.2967
3 1TAD ALF 3.2967
4 1MH1 GNP 3.2967
5 2WKQ GTP 3.2967
6 5XC5 GTP 3.40909
7 1O3Y GTP 4.21687
8 1J2J GTP 4.21687
9 3Q72 GNP 4.21687
10 3RWO GDP 4.32432
11 1RYH GNP 4.4335
12 1Z08 GNP 4.70588
13 4HDO GNP 4.94506
14 1RE0 GDP 4.97738
15 5XKT GNP 5
16 2ZEJ GDP 5.07614
17 1VG9 GDP 5.40541
18 1VG1 GDP 5.40541
19 1GOT GDP 5.49451
20 1G4U GDP 5.49451
21 3T1O GDP 5.55556
22 1WF3 GNP 5.58376
23 5KDO GDP 5.58376
24 6CRK GDP 5.6338
25 1GP2 GDP 5.6338
26 1YRB GDP 5.72519
27 1BH2 GSP 6.03175
28 5M04 GDP 6.04396
29 3CX8 GSP 6.85279
30 5O2T GSP 6.95187
31 2RCN GDP 7.1066
32 1FZQ GDP 7.18232
33 4LC1 GDP 7.4184
34 1ZJ6 G3D 7.48663
35 2W2X GSP 7.56757
36 3MD0 GDP 7.60563
37 1OIX GDP 7.69231
38 1OIV GDP 7.69231
39 1TQ4 GDP 7.69231
40 1KMQ GNP 7.69231
41 1OW3 GDP 7.77202
42 3TK1 GDP 7.87879
43 2C5L GTP 8.09249
44 2HV8 GTP 8.13953
45 1MR3 G3D 8.28729
46 5O74 GDP 8.33333
47 1DS6 GDP 8.33333
48 1I4D GDP 8.33333
49 1E96 GTP 8.37438
50 4U5X GNP 8.42697
51 1CLU DBG 8.43373
52 1PUJ GNP 8.51064
53 4HI0 GDP 8.54271
54 1Z0K GTP 8.72093
55 4DCT GDP 8.88325
56 1S8F GDP 8.88325
57 1YZG GDP 8.93855
58 2FJU GSP 8.98876
59 1R4A GNP 9.09091
60 1M7B GTP 9.23913
61 6D5V GNP 9.34066
62 1YVD GNP 9.46746
63 4BAS GNP 10.0503
64 3Q85 GNP 10.0592
65 5CK5 GDP 10.1266
66 6D5J GNP 10.1796
67 6D5E GNP 10.1796
68 6D59 GNP 10.1796
69 6BVJ GNP 10.1796
70 6BVL GNP 10.1796
71 6D56 GNP 10.1796
72 6BVI GNP 10.1796
73 6BVK GNP 10.1796
74 6D5G GNP 10.1796
75 6D5H GNP 10.1796
76 2QTV GNP 10.2041
77 1WQ1 GDP 10.241
78 3GJ8 GDP 10.4072
79 3GJ0 GDP 10.4072
80 3GJ3 GDP 10.4072
81 3GJ4 GDP 10.4072
82 3GJ5 GDP 10.4072
83 2CJW GDP 10.4167
84 5BXQ GDP 10.6481
85 2A9K GDP 10.6952
86 5HCN GCP 10.989
87 2FFQ GSP 11.1111
88 6AU6 GDP 11.1675
89 3GJ7 GDP 11.2245
90 1ZC3 GNP 11.4286
91 1S9D GDP 11.5385
92 3T12 GDP ALF 11.7647
93 1U8Z GDP 11.9048
94 2A5J GDP 12.0419
95 3M1I GTP 12.0879
96 2WIC GNP 12.3596
97 1CS4 GSP 12.6904
98 1Z2A GDP 13.0952
99 4NON GDP 13.1868
100 1Z0A GDP 13.2184
101 1SVI GDP 13.3333
102 2HT6 GDP 13.4518
103 3T5G GDP 13.8158
104 5TB5 GDP 14
105 3RAB GNP 14.7929
106 1WA5 GTP 14.8352
107 5HPY GDP 14.8352
108 1G16 GDP 15.2941
109 5UWQ GNP 15.3846
110 5UWP GNP 15.3846
111 5UWU GNP 15.3846
112 6CIT GNP 15.3846
113 5UWH GNP 15.3846
114 5UWS GNP 15.3846
115 5UWO GNP 15.3846
116 5UWW GNP 15.3846
117 5UWT GNP 15.3846
118 1G7S GDP 15.4822
119 3EC1 GDP 15.4822
120 4HAT GNP 15.7143
121 4B47 GDP 15.978
122 1F6B GDP 16.1616
123 1UPT GTP 16.6667
124 2OM2 GDP 16.6667
125 2NGR GDP 17.033
126 4DID GDP 17.033
127 1CXZ GSP 17.4419
128 3W5J GDP 17.5127
129 1DAR GDP 18.1319
130 1KSH GDP 18.2796
131 3BC1 GNP 18.4615
132 1MKY GDP 19.5431
133 1ZD9 GDP 19.6809
134 4R98 GNH 19.9262
135 1GUA GNP 21.5569
136 1Z0J GTP 22.0339
137 6G14 G4P 24.3655
138 2WJG GDP 26.0638
139 3CH5 GDP 28.8462
140 2WJH GDP 29.5181
141 5FG3 GDP 29.6954
142 5DIF GNP 31.5789
143 5YT0 GDP 31.5934
144 2QN6 GDP 36.0406
145 1KK1 GNP 42.3858
146 1Y3A GDP 50
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