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Receptor
PDB id Resolution Class Description Source Keywords
2D3Y 1.55 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM THERMUS THE HB8 THERMUS THERMOPHILUS BASE EXCISION REPAIR URACIL-DNA GLYCOSYLASE IRON/SULFER CLTHERMOPHILE STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAGENOMICS/PROTEOMICS INITIATIVE RSGI HYDROLASE
Ref.: CRYSTAL STRUCTURE OF FAMILY 5 URACIL-DNA GLYCOSYLAS TO DNA. J.MOL.BIOL. V. 373 839 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:222;
A:223;
 Invalid;
Invalid;
 none;
none;
 submit data
59.044 C2 H3 O2 CC(=O...
DU A:221;
 Valid;
 none;
 submit data
308.182 C9 H13 N2 O8 P C1[C@...
SF4 A:220;
 Part of Protein;
 none;
 submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2D3Y 1.55 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE FROM THERMUS THE HB8 THERMUS THERMOPHILUS BASE EXCISION REPAIR URACIL-DNA GLYCOSYLASE IRON/SULFER CLTHERMOPHILE STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAGENOMICS/PROTEOMICS INITIATIVE RSGI HYDROLASE
Ref.: CRYSTAL STRUCTURE OF FAMILY 5 URACIL-DNA GLYCOSYLAS TO DNA. J.MOL.BIOL. V. 373 839 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2D3Y - DU C9 H13 N2 O8 P C1[C@@H]([....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2D3Y - DU C9 H13 N2 O8 P C1[C@@H]([....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2D3Y - DU C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DU; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 DU 1 1
2 UMP 1 1
3 DUD 0.8 0.985075
4 UC5 0.772727 0.970588
5 DUT 0.753623 0.985075
6 DUN 0.75 0.956522
7 DUP 0.742857 0.956522
8 DUS 0.692308 0.853333
9 DUR 0.683333 0.852941
10 DDN 0.632353 1
11 UFP 0.591549 0.929577
12 TMP 0.583333 0.956522
13 BRU 0.583333 0.929577
14 5HU 0.583333 0.942857
15 UM3 0.57971 0.955224
16 5IU 0.575342 0.929577
17 DC 0.561644 0.928571
18 DCM 0.561644 0.928571
19 BVP 0.531646 0.942857
20 DU DU DU DU BRU DU DU 0.53125 0.864865
21 U 0.527778 0.911765
22 U5P 0.527778 0.911765
23 DDU 0.523077 0.753623
24 UMC 0.520548 0.941176
25 QBT 0.493333 0.927536
26 DUA 0.487805 0.783784
27 DU3 0.487805 0.780822
28 DU4 0.47619 0.76
29 TYD 0.469136 0.942857
30 YYY 0.451219 0.915493
31 UDP 0.45 0.898551
32 TTP 0.447059 0.942857
33 8OG 0.435294 0.835443
34 U3P 0.434211 0.897059
35 UA3 0.434211 0.897059
36 U2P 0.434211 0.884058
37 UTP 0.433735 0.898551
38 44P 0.43038 0.914286
39 DCP 0.430233 0.915493
40 2KH 0.411765 0.873239
41 DUX 0.411765 0.756757
42 UMF 0.410256 0.84507
43 139 0.409091 0.8
44 UPU 0.409091 0.871429
45 URI 0.408451 0.771429
46 TBD 0.406977 0.90411
47 DU DU DU DU BRU DA DU 0.40625 0.771084
48 PUA 0.405172 0.833333
49 UNP 0.402299 0.873239
50 UDX 0.4 0.873239
51 PUP 0.4 0.955882
52 UAD 0.4 0.873239
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2D3Y; Ligand: DU; Similar sites found with APoc: 186
This union binding pocket(no: 1) in the query (biounit: 2d3y.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 6FIV 3TL None
2 1Q3P GLU ALA GLN THR ARG LEU None
3 4B2H C3F None
4 3VBK COA 0.97561
5 3D91 REM 1.82648
6 1RO7 CSF 1.82648
7 1P4A PCP 1.82648
8 5O4J SAH 1.82648
9 5O4J PJL 1.82648
10 5O4J 9KH 1.82648
11 5DBV COA 2.28311
12 2OG7 AHB 2.28311
13 2Q2V NAD 2.28311
14 4YNM SAM 2.28311
15 1V84 UDP 2.28311
16 3DUW SAH 2.28311
17 6AIX A3P 2.73973
18 3W2E NAD 2.73973
19 3W2E FAD 2.73973
20 5L13 6ZE 2.73973
21 5MRH Q9Z 2.73973
22 5MF5 C2E 2.73973
23 3D9F N6C 2.73973
24 3D9F FAD 2.73973
25 6A5K SAM 2.73973
26 1O9J NAD 2.73973
27 2OJW ADP 2.73973
28 3IVV ASP GLU VAL THR SER THR THR SER SER SER 2.75862
29 2BMZ XLM 2.83688
30 1D01 ACE MET LEU SER VAL GLU GLU GLU GLY 2.97619
31 4UA3 COA 3.09278
32 5ETR 5RW 3.10559
33 5ETR APC 3.10559
34 1JUV NDP 3.10881
35 3HKW IX6 3.19635
36 4MIB 28M 3.19635
37 3GE7 AFQ 3.19635
38 4O6M C5P 3.19635
39 5FA5 MTA 3.19635
40 3RHJ NAP 3.19635
41 4LJ3 C2E 3.19635
42 2AHR NAP 3.19635
43 5SWB NAG BMA MAN MAN MAN MAN 3.19635
44 4OAG ADP 3.19635
45 2QCS ANP 3.19635
46 1X1T NAD 3.19635
47 3AKI AH8 3.19635
48 5D9J 0N8 3.20856
49 2VGD XYP XYP XYP FX3 3.21101
50 3B82 NAD 3.38164
51 2GKS ADP 3.65297
52 1ZPT FAD 3.65297
53 2VK4 TPP 3.65297
54 5KF6 NAD 3.65297
55 5HSA FAS 3.65297
56 5V22 SAH 3.65297
57 3NK7 SAM 3.65297
58 2D4V NAD 3.65297
59 5JLB SAH 3.65297
60 2CFD R4A 3.65297
61 4I3V NAD 3.65297
62 4GKV NAD 3.65297
63 3AFH GSU 3.65297
64 6F05 GTS 3.72093
65 2ODE ALF GDP 4.10959
66 1EBF NAD 4.10959
67 5EOW FAD 4.10959
68 3VC1 SAH 4.10959
69 4ZUL UN1 4.10959
70 3QOX SAH 4.10959
71 5LFV SIA GAL NAG 4.10959
72 2B8T THM 4.10959
73 4JAL SAH 4.19162
74 4WJT NAG 4.19162
75 1KZL CRM 4.32692
76 5DHU 5A8 4.41176
77 1UXG FUM 4.56621
78 1UXG NAD 4.56621
79 5FHD ADP ALF 4.56621
80 4KWI NAP 4.56621
81 4KWI 1TJ 4.56621
82 4PSW COA 4.56621
83 2WME NAP 4.56621
84 5EOU ATP 4.56621
85 4U9W COA 4.83092
86 1T57 FMN 4.85437
87 4KOT CE3 4.93827
88 2FXU BID 5.02283
89 1YKJ FAD 5.02283
90 1YKJ PHB 5.02283
91 1QAN SAH 5.02283
92 4OE4 NAD 5.02283
93 3IWK NAD 5.02283
94 6B5K TYD 5.02283
95 4R84 CSF 5.02283
96 5D4V SAH 5.02283
97 5CSS G3P 5.02283
98 5FRD COA 5.02283
99 2Y4O DLL 5.02283
100 3IWJ NAD 5.02283
101 5FPE 3TR 5.02283
102 2QX0 APC 5.03145
103 5W7U GY8 5.07614
104 3N3T C2E 5.44218
105 4GID 0GH 5.47945
106 2IMP NAI 5.47945
107 5EB4 FAD 5.47945
108 2RGJ FAD 5.47945
109 2ZKJ ADP 5.47945
110 1I1D 16G 5.59006
111 2CNT COA 5.625
112 3MQG ACO 5.72917
113 3HV8 C2E 5.93607
114 5JFL NAD 5.93607
115 5WO4 B7V 5.93607
116 2B4Q NAP 5.93607
117 2QE0 NAP 5.93607
118 5LW0 AR6 6.06061
119 2PID YSA 6.39269
120 4FBL SPD 6.39269
121 3L4S 3PG 6.39269
122 3L4S NAD 6.39269
123 1QZY TDE 6.39269
124 4I8P NAD 6.39269
125 6BCA GSP 6.62252
126 5Y6Q MCN 6.79012
127 2Z4T C5P 6.84932
128 6B5G CQY 6.84932
129 6B5G NAD 6.84932
130 3QSB 743 6.84932
131 4B7X NAP 6.84932
132 5X1M THG 6.84932
133 5X1M DHB 6.84932
134 4NTC FAD 6.84932
135 3FHI ANP 7.14286
136 1USF NAP 7.30337
137 4R5Z SIN 7.30594
138 6EMU SAM 7.30594
139 4TWP AXI 7.30594
140 2QTZ FAD 7.30594
141 2QTZ NAP 7.30594
142 4P8K FAD 7.30594
143 3C6K SPD 7.30594
144 3C6K MTA 7.30594
145 5VSM 5AD 7.76256
146 5VSM MET 7.76256
147 4QLX FMN 7.76256
148 1KRR ACO 7.88177
149 3DR4 G4M 8.21918
150 3NUG NAD 8.6758
151 5H3A UMP 8.6758
152 5OVV ACE ILE GLU SER THR GLU ILE 8.94309
153 5LXT GTP 9.09091
154 1TMM HHR 9.49367
155 1TMM APC 9.49367
156 6MVU K4V 9.58904
157 3AR5 TM1 9.58904
158 5G09 6DF 9.58904
159 5N81 8Q2 9.58904
160 4FJU NAI 9.58904
161 2GTE VA 9.67742
162 2QQC AG2 9.82143
163 2ZWI C5P 10.0457
164 5IUW IAC 10.0457
165 5IUW NAD 10.0457
166 5UPK GNP 10.2703
167 3ICC NAP 10.5023
168 5F1V 3VN 10.5023
169 4PZ2 NAD 10.9589
170 1FIQ FAD 10.9589
171 3NRZ FAD 10.9589
172 5BVE 4VG 10.9589
173 2WTX VDO 10.9589
174 2WTX UDP 10.9589
175 5OVC ACE GLU ALA GLN THR ARG LEU 11.4583
176 2Y5D NAP 11.8721
177 1F0X FAD 11.8721
178 1FQJ ALF 11.9048
179 3QX9 ATP 12.3188
180 4LEB THR THR THR THR THR THR THR 12.3288
181 6MPT C30 12.3288
182 5J6A P46 12.7854
183 5F7Y GLC GAL NAG GAL FUC A2G 15.0685
184 4YFB PAC 17.3516
185 4V3C C 19.1781
186 1WAP TRP 24
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