Receptor
PDB id Resolution Class Description Source Keywords
2PAR 2.1 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF THE 5'-DEOXYNUCLEOTIDASE YFBR MUTANT E7 COMPLEXED WITH CO(2+) AND TMP ESCHERICHIA COLI NUCLEOTIDASE 5-prime -DEOXYNUCLEOTIDASE YFBR HD DOMAIN PHOSPHOHHYDROLASE
Ref.: STRUCTURAL INSIGHT INTO THE MECHANISM OF SUBSTRATE SPECIFICITY AND CATALYTIC ACTIVITY OF AN HD-DOMAIN PHOSPHOHYDROLASE: THE 5'-DEOXYRIBONUCLEOTIDASE YFBR ESCHERICHIA COLI. J.MOL.BIOL. V. 378 215 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CO A:201;
B:201;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.933 Co [Co+2...
PEG A:401;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
TMP A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
322.208 C10 H15 N2 O8 P CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PAR 2.1 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF THE 5'-DEOXYNUCLEOTIDASE YFBR MUTANT E7 COMPLEXED WITH CO(2+) AND TMP ESCHERICHIA COLI NUCLEOTIDASE 5-prime -DEOXYNUCLEOTIDASE YFBR HD DOMAIN PHOSPHOHHYDROLASE
Ref.: STRUCTURAL INSIGHT INTO THE MECHANISM OF SUBSTRATE SPECIFICITY AND CATALYTIC ACTIVITY OF AN HD-DOMAIN PHOSPHOHYDROLASE: THE 5'-DEOXYRIBONUCLEOTIDASE YFBR ESCHERICHIA COLI. J.MOL.BIOL. V. 378 215 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2PAU - D5M C10 H14 N5 O6 P c1nc(c2c(n....
2 2PAR - TMP C10 H15 N2 O8 P CC1=CN(C(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2PAU - D5M C10 H14 N5 O6 P c1nc(c2c(n....
2 2PAR - TMP C10 H15 N2 O8 P CC1=CN(C(=....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2PAU - D5M C10 H14 N5 O6 P c1nc(c2c(n....
2 2PAR - TMP C10 H15 N2 O8 P CC1=CN(C(=....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TMP; Similar ligands found: 93
No: Ligand ECFP6 Tc MDL keys Tc
1 TMP 1 1
2 TYD 0.80597 0.985714
3 TTP 0.760563 0.985714
4 UFP 0.716418 0.917808
5 TBD 0.708333 0.945205
6 BRU 0.705882 0.917808
7 5HU 0.705882 0.957747
8 TTP MG 0.702703 0.957143
9 5IU 0.695652 0.917808
10 THM 0.693548 0.859155
11 LLT 0.693548 0.859155
12 NYM 0.671429 0.971831
13 FDM 0.671429 0.931507
14 THP 0.661972 0.985507
15 TLO 0.654321 0.931507
16 9RC 0.646341 0.839506
17 0DN 0.646154 0.84507
18 BVP 0.64 0.957747
19 ATM 0.64 0.906667
20 DAU 0.635294 0.918919
21 18T 0.623529 0.918919
22 TRH 0.623529 0.918919
23 1JB 0.623529 0.918919
24 TDX 0.623529 0.931507
25 3R2 0.623529 0.906667
26 3YN 0.609195 0.918919
27 DWN 0.609195 0.894737
28 T3Q 0.609195 0.894737
29 T3F 0.609195 0.894737
30 0N2 0.602273 0.883117
31 T46 0.602273 0.918919
32 T3P 0.6 0.957143
33 0FX 0.595506 0.894737
34 MMF 0.595506 0.894737
35 AKM 0.593407 0.873418
36 UMP 0.583333 0.956522
37 DU 0.583333 0.956522
38 QDM 0.582418 0.883117
39 JHZ 0.576087 0.871795
40 1YF 0.576087 0.906667
41 FNF 0.576087 0.906667
42 TXS 0.575342 0.8
43 4TG 0.569892 0.906667
44 5CM 0.565789 0.931507
45 T3S 0.56 0.8
46 2DT 0.555556 0.971429
47 3DR DT DT DT DT DT 0.553191 0.917808
48 ATY 0.548781 0.931507
49 DDN 0.547945 0.956522
50 AZD 0.535714 0.894737
51 FUH 0.53 0.894737
52 QUH 0.53 0.894737
53 T5A 0.524272 0.829268
54 DT ME6 DT 0.509804 0.881579
55 DC 0.506494 0.890411
56 DCM 0.506494 0.890411
57 AZZ 0.5 0.789474
58 4TA 0.495327 0.817073
59 ABT 0.483516 0.871795
60 QBT 0.480519 0.915493
61 WMJ 0.477778 0.75
62 ADS THS THS THS 0.477477 0.767442
63 TQP 0.474138 0.851852
64 7SG 0.474138 0.851852
65 T4K 0.470085 0.841463
66 T5K 0.470085 0.841463
67 DUD 0.469136 0.942857
68 UMC 0.467532 0.901408
69 D3T 0.464286 0.957747
70 TPE 0.463158 0.881579
71 D4M 0.461538 0.927536
72 ID2 0.452055 0.786667
73 UC5 0.451219 0.929577
74 DUT 0.447059 0.942857
75 DUP 0.44186 0.916667
76 DUN 0.440476 0.916667
77 DT MA7 DT 0.42623 0.807229
78 8OG 0.425287 0.82716
79 BVD 0.423077 0.821918
80 74W 0.42 0.72093
81 74X 0.42 0.72093
82 O5W 0.417391 0.831325
83 5FU 0.4125 0.84
84 D4D 0.411765 0.914286
85 DUT MG 0.409091 0.914286
86 PAX 0.408333 0.839506
87 YYY 0.406977 0.878378
88 BTD 0.404762 0.759494
89 DPB 0.404494 0.890411
90 5BU 0.402439 0.84
91 3DT 0.4 0.821918
92 UMP AF3 PO4 0.4 0.842105
93 DUS 0.4 0.820513
Similar Ligands (3D)
Ligand no: 1; Ligand: TMP; Similar ligands found: 256
No: Ligand Similarity coefficient
1 U5P 0.9732
2 U 0.9715
3 9L3 0.9664
4 C 0.9658
5 TKW 0.9632
6 C5P 0.9620
7 CAR 0.9605
8 DOC 0.9594
9 DI 0.9588
10 D5M 0.9583
11 DA 0.9583
12 AS 0.9562
13 FN5 0.9539
14 PSU 0.9510
15 AMP 0.9498
16 5HM 0.9493
17 UP6 0.9493
18 CNU 0.9453
19 G 0.9439
20 FNU 0.9424
21 BMP 0.9421
22 71V 0.9416
23 CH 0.9402
24 DGP 0.9400
25 DG 0.9399
26 IRP 0.9398
27 IMP 0.9395
28 AMP MG 0.9392
29 NUP 0.9391
30 H2U 0.9386
31 BMQ 0.9386
32 45A 0.9357
33 FMP 0.9350
34 16B 0.9328
35 8BR 0.9313
36 SRA 0.9310
37 U6M 0.9302
38 S5P 0.9291
39 5GP 0.9283
40 6MA 0.9256
41 NIA 0.9236
42 1RB 0.9232
43 XMP 0.9225
44 NCN 0.9209
45 PFU 0.9208
46 AMZ 0.9203
47 NMN 0.9201
48 IMU 0.9179
49 C2R 0.9163
50 7D5 0.9156
51 M2T 0.9153
52 AIR 0.9142
53 IGP 0.9119
54 7RP 0.9113
55 ZAS 0.9112
56 O7E 0.9111
57 G7M 0.9109
58 Z8B 0.9107
59 AOC 0.9102
60 P2P 0.9102
61 MTI 0.9099
62 MTM 0.9089
63 EP4 0.9078
64 7RA 0.9076
65 8OP 0.9075
66 JW5 0.9074
67 U4S 0.9067
68 NEC 0.9060
69 103 0.9052
70 6CN 0.9050
71 CMP 0.9048
72 8GM 0.9041
73 PCG 0.9018
74 N5O 0.9014
75 MTH 0.9008
76 6RE 0.9008
77 J7C 0.9008
78 6AU 0.8994
79 X29 0.8993
80 AAM 0.8992
81 MTA 0.8986
82 4BH 0.8983
83 T7O 0.8981
84 101 0.8975
85 3RC 0.8971
86 IWH 0.8953
87 93A 0.8949
88 CDP 0.8942
89 OMP 0.8940
90 RBZ 0.8940
91 RMB 0.8940
92 SP1 0.8938
93 NWQ 0.8937
94 A3N 0.8927
95 0RA 0.8924
96 35G 0.8923
97 RP1 0.8922
98 3F5 0.8922
99 SNP 0.8911
100 4X2 0.8911
101 5AS 0.8909
102 QTJ 0.8907
103 FAI 0.8897
104 U3S 0.8891
105 N8M 0.8882
106 K8W 0.8865
107 O8M 0.8865
108 P1D 0.8862
109 HDU 0.8860
110 JLN 0.8858
111 F9B 0.8856
112 2GE 0.8854
113 9X0 0.8850
114 9W7 0.8846
115 U1S 0.8844
116 VIB 0.8841
117 6SZ 0.8839
118 U2S 0.8839
119 MCF 0.8838
120 9RK 0.8834
121 S2X 0.8832
122 2OM 0.8831
123 JP3 0.8828
124 KWV 0.8825
125 E42 0.8823
126 6SW 0.8823
127 AZU 0.8821
128 5QT 0.8817
129 7CH 0.8816
130 DRM 0.8814
131 TRP GLY 0.8811
132 IRN 0.8803
133 3GP 0.8801
134 1Q2 0.8801
135 41L 0.8798
136 M8Q 0.8796
137 PZB 0.8789
138 HGH 0.8788
139 AHU 0.8779
140 34L 0.8779
141 CMZ 0.8774
142 MN QAY 0.8774
143 GAR 0.8772
144 43J 0.8771
145 JFX 0.8768
146 FIP 0.8763
147 TMC 0.8763
148 SSI 0.8762
149 6SX 0.8756
150 B86 0.8754
151 6SY 0.8753
152 75G 0.8753
153 1CE 0.8750
154 SU1 0.8748
155 6J7 0.8748
156 4JW 0.8743
157 PCP 0.8742
158 KWD 0.8741
159 RKY 0.8739
160 S0J 0.8736
161 A3S 0.8725
162 13F 0.8724
163 5BT 0.8722
164 2AM 0.8719
165 9PP 0.8716
166 MCY 0.8716
167 MTE 0.8715
168 P2G 0.8715
169 FO2 0.8712
170 PNW 0.8711
171 C4F 0.8711
172 100 0.8711
173 VCE 0.8709
174 RFZ 0.8708
175 VM7 0.8705
176 460 0.8702
177 QTM 0.8700
178 43G 0.8700
179 FOY 0.8700
180 SCT 0.8699
181 67B 0.8699
182 K6B 0.8698
183 BXS 0.8696
184 7KE 0.8696
185 O7M 0.8691
186 VKE 0.8688
187 9W8 0.8687
188 6U5 0.8686
189 U55 0.8686
190 BO1 0.8683
191 DZJ 0.8678
192 3D1 0.8676
193 IPL 0.8672
194 ZKW 0.8671
195 5NB 0.8670
196 BFS 0.8668
197 BY0 0.8667
198 2T4 0.8663
199 1E5 0.8658
200 NOS 0.8656
201 9K2 0.8655
202 OVE 0.8654
203 PNJ 0.8651
204 C0V 0.8649
205 PY1 0.8649
206 R38 0.8648
207 KMG 0.8647
208 ADN 0.8647
209 UDP 0.8642
210 7G2 0.8642
211 EFX 0.8639
212 KVQ 0.8638
213 90J 0.8637
214 CHV 0.8634
215 QC2 0.8634
216 PMO 0.8631
217 0DJ 0.8627
218 AQ1 0.8626
219 NFG 0.8622
220 IMH 0.8621
221 6XR 0.8618
222 GMP 0.8611
223 7VF 0.8610
224 0LA 0.8606
225 FYK 0.8605
226 PRX 0.8602
227 N1Y 0.8602
228 F01 0.8599
229 ADL 0.8596
230 ESJ 0.8593
231 E44 0.8591
232 Q7U 0.8591
233 DUR 0.8589
234 65W 0.8588
235 FT1 0.8586
236 GG5 0.8585
237 CTN 0.8584
238 DCZ 0.8583
239 PB2 0.8582
240 5UD 0.8582
241 TVC 0.8577
242 TAL 0.8570
243 E2N 0.8569
244 KVW 0.8566
245 4ZW 0.8564
246 802 0.8560
247 LMZ 0.8555
248 0NH 0.8554
249 8MF 0.8552
250 5V3 0.8550
251 KUQ 0.8549
252 FT3 0.8547
253 FMC 0.8545
254 SDN 0.8536
255 6MY 0.8534
256 I5A 0.8529
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2par.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2par.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2par.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2par.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2par.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2par.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2par.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2PAR; Ligand: TMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 2par.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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