Receptor
PDB id Resolution Class Description Source Keywords
3MKN 2 Å EC: 3.2.2.8 CRYSTAL STRUCTURE OF THE E. COLI PYRIMIDINE NUCLEOSIDASE YEI A COMPETITIVE INHIBITOR ESCHERICHIA COLI PYRIMIDINE NUCLEOSIDE HYDROLASE NUCLEOTIDE METABOLISM ENZYINHIBITOR COMPLEX METALLOENZYME HYDROLASE-HYDROLASE INHIBCOMPLEX
Ref.: ENERGY LANDSCAPES ASSOCIATED WITH MACROMOLECULAR CONFORMATIONAL CHANGES FROM ENDPOINT STRUCTURES J.AM.CHEM.SOC. V. 132 17570 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:501;
B:501;
C:501;
D:501;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
DNB A:502;
B:502;
C:502;
D:502;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 76 uM
239.271 C11 H17 N3 O3 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3MKN 2 Å EC: 3.2.2.8 CRYSTAL STRUCTURE OF THE E. COLI PYRIMIDINE NUCLEOSIDASE YEI A COMPETITIVE INHIBITOR ESCHERICHIA COLI PYRIMIDINE NUCLEOSIDE HYDROLASE NUCLEOTIDE METABOLISM ENZYINHIBITOR COMPLEX METALLOENZYME HYDROLASE-HYDROLASE INHIBCOMPLEX
Ref.: ENERGY LANDSCAPES ASSOCIATED WITH MACROMOLECULAR CONFORMATIONAL CHANGES FROM ENDPOINT STRUCTURES J.AM.CHEM.SOC. V. 132 17570 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3MKN Ki = 76 uM DNB C11 H17 N3 O3 c1cc(c(cc1....
2 3B9X - NOS C10 H12 N4 O5 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3MKN Ki = 76 uM DNB C11 H17 N3 O3 c1cc(c(cc1....
2 3B9X - NOS C10 H12 N4 O5 c1nc2c(n1[....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2MAS Kd = 30 nM PIR C11 H16 N2 O3 c1cc(ccc1[....
2 1YOE - RIB C5 H10 O5 C([C@@H]1[....
3 3G5I - DNB C11 H17 N3 O3 c1cc(c(cc1....
4 3MKN Ki = 76 uM DNB C11 H17 N3 O3 c1cc(c(cc1....
5 3B9X - NOS C10 H12 N4 O5 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DNB; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 DNB 1 1
2 PIR 0.55102 0.954545
Similar Ligands (3D)
Ligand no: 1; Ligand: DNB; Similar ligands found: 272
No: Ligand Similarity coefficient
1 ADN 0.9602
2 NOS 0.9562
3 TBN 0.9512
4 FMC 0.9450
5 FM1 0.9432
6 CTN 0.9413
7 MTA 0.9403
8 FMB 0.9401
9 THM 0.9379
10 TAL 0.9378
11 0DN 0.9375
12 PUR 0.9372
13 ZEB 0.9361
14 URI 0.9356
15 2TU 0.9346
16 DHZ 0.9321
17 5UD 0.9320
18 MCY 0.9295
19 DCZ 0.9290
20 FM2 0.9260
21 TYU 0.9248
22 IMH 0.9242
23 B86 0.9241
24 ID2 0.9237
25 MDR 0.9235
26 2FA 0.9234
27 DUR 0.9226
28 GMP 0.9220
29 49O 0.9201
30 XYA 0.9201
31 5BT 0.9199
32 MTP 0.9180
33 URD 0.9180
34 CTD 0.9163
35 W29 0.9152
36 JRB 0.9146
37 THU 0.9145
38 RBV 0.9133
39 B2Y 0.9128
40 61O 0.9127
41 A 0.9123
42 ANU 0.9118
43 K80 0.9116
44 GTC 0.9106
45 5VL 0.9104
46 6CR 0.9090
47 BRD 0.9087
48 MPK 0.9083
49 SV4 0.9081
50 CH9 0.9078
51 5AD 0.9073
52 1DA 0.9072
53 PQT 0.9050
54 PJW 0.9047
55 MTM 0.9042
56 I5A 0.9037
57 GEO 0.9037
58 3D1 0.9035
59 MOK 0.9031
60 PRH 0.9028
61 6HX 0.9026
62 HNK 0.9014
63 BP3 0.9013
64 5NB 0.9010
65 HJH 0.9009
66 2FD 0.9007
67 9UL 0.8999
68 RAB 0.8997
69 HPR 0.8992
70 SLY 0.8985
71 1WC 0.8981
72 9W5 0.8977
73 4WF 0.8973
74 5E4 0.8967
75 BDJ 0.8966
76 RIS 0.8966
77 NNR 0.8958
78 N8Z 0.8952
79 OBP 0.8949
80 WOE 0.8948
81 5AE 0.8947
82 ID8 0.8942
83 C0H 0.8942
84 BPY 0.8941
85 3DT 0.8941
86 CH8 0.8936
87 MTH 0.8935
88 FPL 0.8932
89 AD3 0.8930
90 XDK 0.8926
91 ING 0.8925
92 RLG 0.8920
93 F16 0.8918
94 2B4 0.8918
95 DBM 0.8916
96 U2Z 0.8916
97 DE3 0.8915
98 SQP 0.8907
99 A1Y 0.8906
100 BPS 0.8904
101 MJ5 0.8893
102 49N 0.8890
103 5JT 0.8890
104 9PL 0.8889
105 89J 0.8888
106 NQ7 0.8887
107 7Q1 0.8885
108 NI9 0.8878
109 B4O 0.8873
110 BP6 0.8869
111 JVQ 0.8867
112 DAH 0.8865
113 Y3J 0.8863
114 7ZL 0.8862
115 A3Q 0.8861
116 A9O 0.8857
117 GFE 0.8857
118 A7K 0.8857
119 MZR 0.8856
120 YOF 0.8854
121 3B4 0.8854
122 DC5 0.8854
123 L13 0.8847
124 60Q 0.8847
125 A6H 0.8845
126 A4D 0.8844
127 0OO 0.8843
128 977 0.8835
129 9DI 0.8833
130 DDU 0.8832
131 0A9 0.8830
132 458 0.8828
133 T2D 0.8827
134 AVI 0.8827
135 A4Q 0.8824
136 CP6 0.8823
137 BTM 0.8821
138 GL2 0.8821
139 X11 0.8819
140 5N5 0.8818
141 NIR 0.8815
142 CMU 0.8814
143 QUS 0.8813
144 CWD 0.8812
145 A4T 0.8809
146 A9K 0.8802
147 ZOL 0.8799
148 FWD 0.8799
149 46P 0.8798
150 GL7 0.8781
151 3QO 0.8779
152 6J9 0.8779
153 1Z8 0.8776
154 BZQ 0.8775
155 EXG 0.8775
156 TH4 0.8775
157 EAJ 0.8772
158 3AD 0.8772
159 KYN 0.8771
160 MIL 0.8770
161 A4N 0.8766
162 6HO 0.8766
163 CLU 0.8765
164 B2T 0.8761
165 TRP 0.8760
166 16Z 0.8756
167 1ZC 0.8755
168 AKD 0.8752
169 7QS 0.8752
170 ACE PHE 0.8749
171 5CD 0.8745
172 5FD 0.8744
173 CC5 0.8743
174 TIZ 0.8740
175 HNH 0.8738
176 IM4 0.8736
177 BCK 0.8735
178 TCL 0.8735
179 54F 0.8732
180 S0G 0.8726
181 7VY 0.8723
182 GLS 0.8720
183 RFZ 0.8717
184 AVJ 0.8712
185 N1Y 0.8712
186 S3C 0.8712
187 HFA 0.8709
188 CK2 0.8708
189 BWD 0.8707
190 78U 0.8703
191 50Q 0.8703
192 C2M 0.8702
193 AWE 0.8700
194 1A7 0.8694
195 50C 0.8693
196 FNA 0.8693
197 CK1 0.8691
198 A9P 0.8689
199 ZIQ 0.8687
200 XFE 0.8686
201 1VK 0.8685
202 2LT 0.8684
203 HNL 0.8682
204 4UO 0.8681
205 1XA 0.8680
206 GL5 0.8679
207 F5F 0.8677
208 1CY 0.8670
209 5F1 0.8667
210 MTI 0.8665
211 TI7 0.8663
212 54E 0.8661
213 IYR 0.8660
214 R9J 0.8658
215 MXD 0.8658
216 4GU 0.8657
217 LLT 0.8657
218 GL4 0.8654
219 S7V 0.8654
220 BZS 0.8654
221 HHV 0.8653
222 M0N 0.8651
223 N2Y 0.8647
224 HO6 0.8646
225 M02 0.8646
226 TT4 0.8643
227 IWD 0.8643
228 88R 0.8643
229 R2P 0.8642
230 3RP 0.8641
231 FUZ 0.8636
232 AOT 0.8636
233 PPY 0.8634
234 PHE 0.8632
235 A4B 0.8631
236 AUV 0.8629
237 NWW 0.8626
238 1FF 0.8625
239 S2P 0.8623
240 8OX 0.8622
241 TYR 0.8620
242 7R4 0.8618
243 LT8 0.8616
244 LTT 0.8616
245 42R 0.8611
246 WVV 0.8609
247 DIF 0.8607
248 CL9 0.8602
249 JVN 0.8602
250 ONR 0.8599
251 P2L 0.8595
252 DCF 0.8594
253 JF6 0.8592
254 C6J 0.8590
255 TOH 0.8588
256 RVD 0.8584
257 JA3 0.8583
258 3YQ 0.8573
259 GVG 0.8572
260 TYC 0.8568
261 159 0.8567
262 TR7 0.8565
263 1U7 0.8563
264 9PY 0.8563
265 6MD 0.8552
266 N2Z 0.8549
267 LDC 0.8547
268 AMQ 0.8543
269 HWD 0.8538
270 AMR 0.8537
271 Y4L 0.8523
272 XRS 0.8505
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3MKN; Ligand: DNB; 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: 3mkn.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3MKN; Ligand: DNB; 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: 3mkn.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3MKN; Ligand: DNB; Similar sites found with APoc: 2
This union binding pocket(no: 3) in the query (biounit: 3mkn.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 3EPW JMQ 33.2278
2 3EPW JMQ 33.2278
Pocket No.: 4; Query (leader) PDB : 3MKN; Ligand: DNB; Similar sites found with APoc: 2
This union binding pocket(no: 4) in the query (biounit: 3mkn.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3EPW JMQ 33.2278
2 3EPW JMQ 33.2278
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