Receptor
PDB id Resolution Class Description Source Keywords
1W3R 1.9 Å NON-ENZYME: OTHER NIMA FROM D. RADIODURANS WITH METRONIDAZOLE AND PYRUVATE DEINOCOCCUS RADIODURANS ANTIBIOTIC RESISTANCE DEINOCOCCUS RADIODURANS 5-NITROIMIDARESISTANCE NIM GENE CATALYTIC MECHANISM
Ref.: STRUCTURAL BASIS OF 5-NITROIMIDAZOLE ANTIBIOTIC RES THE CRYSTAL STRUCTURE OF NIMA FROM DEINOCOCCUS RADI J.BIOL.CHEM. V. 279 55840 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2MN A:1198;
Valid;
none;
submit data
171.154 C6 H9 N3 O3 Cc1nc...
ACT A:1196;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
PYR A:1197;
Valid;
none;
submit data
88.062 C3 H4 O3 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1W3R 1.9 Å NON-ENZYME: OTHER NIMA FROM D. RADIODURANS WITH METRONIDAZOLE AND PYRUVATE DEINOCOCCUS RADIODURANS ANTIBIOTIC RESISTANCE DEINOCOCCUS RADIODURANS 5-NITROIMIDARESISTANCE NIM GENE CATALYTIC MECHANISM
Ref.: STRUCTURAL BASIS OF 5-NITROIMIDAZOLE ANTIBIOTIC RES THE CRYSTAL STRUCTURE OF NIMA FROM DEINOCOCCUS RADI J.BIOL.CHEM. V. 279 55840 2004
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 1W3R - PYR C3 H4 O3 CC(=O)C(=O....
2 1W3O - PYR C3 H4 O3 CC(=O)C(=O....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 1W3R - PYR C3 H4 O3 CC(=O)C(=O....
2 1W3O - PYR C3 H4 O3 CC(=O)C(=O....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 1W3R - PYR C3 H4 O3 CC(=O)C(=O....
2 1W3O - PYR C3 H4 O3 CC(=O)C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2MN; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 2MN 1 1
2 1VQ 0.583333 0.6875
3 2VQ 0.583333 0.692308
Ligand no: 2; Ligand: PYR; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PYR 1 1
2 ACY 0.636364 0.636364
3 OXD 0.545455 0.642857
4 KIV 0.411765 0.785714
5 AAE 0.411765 0.625
6 2KT 0.411765 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1W3R; Ligand: 2MN; Similar sites found: 39
This union binding pocket(no: 1) in the query (biounit: 1w3r.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.008112 0.44695 None
2 1H82 GZZ 0.02588 0.40701 1.38889
3 2C31 TZD 0.01175 0.42777 1.85185
4 3GB5 FMN 0.001476 0.41661 1.85185
5 2CFA FAD 0.004539 0.40225 1.85185
6 4NAT ADP 0.03823 0.40878 1.875
7 1MVN PCO 0.0006673 0.47184 1.91388
8 1MVN FMN 0.001747 0.43887 1.91388
9 4M5P MLA 0.005783 0.44524 2.31481
10 1Z44 NPO 0.02145 0.42404 2.31481
11 2WGC SIA GAL BGC 0.005248 0.45717 2.33918
12 3UEC ALA ARG TPO LYS 0.006039 0.42138 2.73973
13 4RJK PYR 0.01094 0.43993 2.77778
14 2D37 FMN 0.002535 0.41826 2.84091
15 1NOX FMN 0.0006499 0.42971 2.92683
16 1H0C AOA 0.006001 0.4215 3.24074
17 3B9Z CO2 0.03563 0.40571 3.24074
18 1RZM E4P 0.01325 0.40591 3.7037
19 1BTN I3P 0.001411 0.49654 3.77358
20 3PY5 AMP 0.002396 0.4026 4.16667
21 4PLG NAI 0.015 0.40037 4.16667
22 4PLG OXM 0.015 0.40037 4.16667
23 1SS4 GSH 0.01651 0.434 4.57516
24 2ZWS PLM 0.00235 0.47599 5.09259
25 1XX4 BAM 0.01961 0.4106 5.09259
26 1TDF NAP 0.01666 0.4206 5.6962
27 2XDQ MGX 0.005629 0.43731 6.01852
28 1M5B BN1 0.008144 0.42641 6.01852
29 1O9U ADZ 0.01096 0.42307 6.01852
30 1ZCH FMN 0.0003873 0.44008 6.94444
31 1VPM COA 0.004164 0.40533 7.10059
32 4P3H 25G 0.008308 0.41737 7.25389
33 2VEZ ACO 0.004487 0.41163 9.47368
34 4CS4 ANP 0.008854 0.40956 9.72222
35 4CS4 AXZ 0.01226 0.40956 9.72222
36 1T0S BML 0.003552 0.43908 10.4651
37 2V5E SCR 0.006775 0.44171 11
38 3S9K CIT 0.01801 0.43366 14.4068
39 1WGC SIA GAL BGC 0.02543 0.41204 18.1287
Pocket No.: 2; Query (leader) PDB : 1W3R; Ligand: PYR; Similar sites found: 207
This union binding pocket(no: 2) in the query (biounit: 1w3r.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4LTN FMN 0.004754 0.46983 None
2 4LTN NAI 0.006944 0.46472 None
3 1POC GEL 0.001797 0.45758 None
4 1UO5 PIH 0.003023 0.44529 None
5 1IM8 SAI 0.02087 0.41194 None
6 1NHZ 486 0.002434 0.4591 0.925926
7 4LSJ LSJ 0.003834 0.44772 0.925926
8 1XX6 ADP 0.007541 0.41899 1.04712
9 4E1N TQX 0.02606 0.40879 1.20482
10 1RYI FAD 0.01013 0.45082 1.38889
11 1RYI GOA 0.01272 0.44748 1.38889
12 1XHL NDP 0.02338 0.42291 1.38889
13 3L02 CP 0.0274 0.41939 1.38889
14 3L02 SN0 0.0274 0.41939 1.38889
15 1LO8 4CA 0.03211 0.43753 1.41844
16 3L1N PLM 0.01116 0.42165 1.54639
17 3GB5 FMN 0.004866 0.44088 1.85185
18 3E9K 3XH 0.009565 0.41165 1.85185
19 2PMP C5P 0.000208 0.49699 1.875
20 1MVN PCO 0.003021 0.48991 1.91388
21 4FDV 0UK 0.00773 0.44733 1.91388
22 1MVN FMN 0.02916 0.4241 1.91388
23 3R35 4CO 0.02711 0.4185 1.98676
24 3BEJ MUF 0.0008361 0.50855 2.31481
25 1XVV CCQ 0.002105 0.48419 2.31481
26 1R6D NAD 0.01727 0.44753 2.31481
27 2VPR TDC 0.02387 0.40202 2.31481
28 2WGC SIA GAL BGC 0.006171 0.42962 2.33918
29 2YVO AMP 0.003565 0.45103 2.74725
30 4RJK PYR 0.001615 0.45906 2.77778
31 1FP1 SAH 0.003002 0.4448 2.77778
32 3O03 NAP 0.006417 0.4448 2.77778
33 3I51 6PL 0.007036 0.44136 2.77778
34 1P72 ADP 0.01638 0.42962 2.77778
35 3MB5 SAM 0.03564 0.42849 2.77778
36 4LWA Q13 0.02988 0.42447 2.77778
37 1V9N NDP 0.02237 0.42389 2.77778
38 4TSK TLA 0.01737 0.41416 2.77778
39 1FP1 HCC 0.01835 0.41125 2.77778
40 1WUR 8DG 0.0262 0.40868 2.77778
41 1DSS NAD 0.03558 0.40635 2.77778
42 2D37 FMN 0.0009768 0.48533 2.84091
43 2D37 NAD 0.002403 0.46746 2.84091
44 1B66 BIO 0.007314 0.43582 2.85714
45 1NOX FMN 0.008262 0.42978 2.92683
46 1X92 M7P 0.001443 0.45495 3.01508
47 1SBZ FMN 0.04096 0.41043 3.04569
48 1V5F FAD 0.03564 0.46118 3.24074
49 1V5F TPP 0.03564 0.46118 3.24074
50 1GRO ICT 0.008013 0.4606 3.24074
51 4DL8 UMP AF3 PO4 0.002079 0.45868 3.24074
52 2DTX BMA 0.00724 0.45647 3.24074
53 1SSQ CYS 0.0154 0.44521 3.24074
54 2YBQ UP2 0.01119 0.44364 3.24074
55 4PO2 ASN ARG LEU LEU LEU THR GLY 0.00704 0.43983 3.24074
56 4C12 ADP 0.02544 0.43779 3.24074
57 1P9P SAH 0.006801 0.43736 3.24074
58 1ZK7 FAD 0.04292 0.42117 3.24074
59 1UAY ADN 0.009653 0.41863 3.24074
60 1ML4 PAL 0.01911 0.41769 3.24074
61 1FDJ 2FP 0.0167 0.40521 3.24074
62 3B9Z CO2 0.01773 0.40383 3.24074
63 3QP4 HL0 0.01823 0.40762 3.2967
64 3LZW FAD 0.0009218 0.50155 3.7037
65 2E2R 2OH 0.005964 0.45542 3.7037
66 3TDC 0EU 0.003227 0.44547 3.7037
67 3P0F BAU 0.003052 0.44446 3.7037
68 2C7G FAD 0.03533 0.43213 3.7037
69 2C7G ODP 0.03435 0.43213 3.7037
70 1WTC ACP 0.005646 0.42961 3.7037
71 1BTN I3P 0.0004623 0.49654 3.77358
72 2A0S BIO 0.004024 0.45098 3.88889
73 2Z9C DTC 0.002269 0.46563 4
74 2Z9C FMN 0.009436 0.42699 4
75 1DKU AP2 0.000665 0.49442 4.16667
76 4PLG NAI 0.009582 0.44815 4.16667
77 4PLG OXM 0.009582 0.44815 4.16667
78 4KCF AKM 0.006674 0.4394 4.16667
79 3AHC TPP 0.01086 0.43741 4.16667
80 3OND ADN 0.02318 0.43699 4.16667
81 3OND NAD 0.02318 0.43699 4.16667
82 2QXX TTP 0.0156 0.43673 4.16667
83 1WVG APR 0.009356 0.43523 4.16667
84 2OD9 A1R NCA 0.01206 0.43512 4.16667
85 3PY5 AMP 0.005151 0.4337 4.16667
86 2F5T MAL 0.006642 0.43249 4.16667
87 2QQF A1R 0.01428 0.42613 4.16667
88 3OZG SSI 0.01276 0.41499 4.16667
89 4KCF FMN 0.01306 0.41451 4.16667
90 1NHK CMP 0.03635 0.40967 4.16667
91 1QRD FAD 0.03835 0.40196 4.16667
92 1SS4 GSH 0.00635 0.434 4.57516
93 4W97 UCA 0.002061 0.46607 4.62963
94 4BJZ FAD 0.03148 0.44255 4.62963
95 4BJZ P3A 0.03148 0.44255 4.62963
96 5H94 LYS MET ASN THR GLN PHE THR ALA VAL 0.005764 0.44086 4.62963
97 3ZY6 GFB 0.007801 0.43275 4.62963
98 1DJ9 KAM 0.0105 0.43127 4.62963
99 1U7Z PMT 0.02426 0.42319 4.62963
100 3RO7 TDR 0.03139 0.41167 4.62963
101 4NE2 ADP 0.045 0.40938 4.62963
102 4NE2 SH2 0.0492 0.40938 4.62963
103 2ZB3 NDP 0.03801 0.40868 4.62963
104 3G4G D71 0.04359 0.40232 4.62963
105 3IIS PID 0.01194 0.46521 4.63576
106 4QBK 3NZ 0.01806 0.41336 4.63918
107 3TCT 3MI 0.03404 0.43098 4.72441
108 2AMV BIN 0.001284 0.50517 5.09259
109 3TN7 NJP 0.005309 0.45434 5.09259
110 1A69 FMB 0.01792 0.45136 5.09259
111 1RYD NDP 0.01421 0.43933 5.09259
112 4FWE FAD 0.02437 0.43262 5.09259
113 1AUA BOG 0.00307 0.43146 5.09259
114 1XOC VAL ASP SER LYS ASN THR SER SER TRP 0.04698 0.41501 5.09259
115 1MDZ PLP 0.03846 0.41184 5.09259
116 3LST SAH 0.01862 0.40514 5.09259
117 2FQO HYI 0.03021 0.40854 5.09554
118 1QCA FUA 0.02897 0.41645 5.16432
119 2WQF FMN 0.009876 0.41592 5.44554
120 2VBQ BSJ 0.03616 0.41533 5.45455
121 4GO7 THR 0.003613 0.43382 5.5
122 2F01 BTN 0.04236 0.43266 5.51181
123 3VHZ L2P GLC MAN SGA 0.005253 0.48318 5.55556
124 1M7Y PPG 0.004414 0.45707 5.55556
125 1ITZ TPP 0.008508 0.43423 5.55556
126 2AE2 NAP 0.02317 0.43116 5.55556
127 2AE2 PTO 0.02317 0.43116 5.55556
128 3RKR NAP 0.005225 0.42886 5.55556
129 2DKH FAD 0.0464 0.40869 5.55556
130 4DEM YS4 0.006994 0.48299 6.01852
131 1PGP 6PG 0.01831 0.43263 6.01852
132 1XNK XS2 0.01748 0.40848 6.12245
133 2V7T SAH 0.008066 0.48257 6.48148
134 1YB5 NAP 0.01168 0.44054 6.48148
135 3PFG SAM 0.03978 0.41883 6.48148
136 3PFG TLO 0.03978 0.41883 6.48148
137 1CL2 PPG 0.01541 0.41667 6.48148
138 3HF3 FMN 0.01954 0.41334 6.48148
139 2FOI JPA 0.01912 0.40016 6.66667
140 1ZCH FMN 0.004795 0.44301 6.94444
141 1KYZ FER 0.01546 0.42713 6.94444
142 1KYZ SAH 0.008586 0.42713 6.94444
143 1VPM COA 0.01464 0.42265 7.10059
144 1MK1 APR 0.01609 0.41907 7.24638
145 4P3H 25G 0.0001248 0.55339 7.25389
146 1S8F GDP 0.009604 0.4361 7.34463
147 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.00277 0.41923 7.40741
148 1PL6 NAD 0.03493 0.40251 7.40741
149 2PY4 DUP 0.02011 0.43391 7.47126
150 1YWQ FMN 0.01409 0.41294 7.5
151 1G0N PHH 0.01151 0.44794 7.77385
152 3V1U NAD 0.02797 0.41159 7.79221
153 2H8Z FMN 0.01074 0.43638 7.87037
154 2H8Z 8CM 0.01074 0.43638 7.87037
155 1UKW FAD 0.03042 0.4222 7.87037
156 2HJ3 FAD 0.007596 0.43332 8
157 3I28 34N 0.01136 0.45261 8.33333
158 3IB8 AMP 0.00278 0.44409 8.33333
159 1R27 MGD 0.02017 0.43047 8.33333
160 3LEO GSH 0.04643 0.40425 8.33333
161 1UW1 ADP 0.003223 0.42739 8.75
162 1A8R GTP 0.005046 0.44012 8.7963
163 1NUS NMN 0.004999 0.46961 9.12698
164 1NUS APC 0.00422 0.46961 9.12698
165 1OLS TDP 0.01095 0.45175 9.25926
166 2JC9 ADN 0.002359 0.43668 9.25926
167 2VEZ G6P 0.04131 0.40801 9.47368
168 2VEZ ACO 0.03918 0.40801 9.47368
169 2NP9 YE1 0.0009476 0.49339 9.72222
170 1H6C SIN 0.007425 0.4559 10.1852
171 1H6C NDP 0.009819 0.4476 10.1852
172 2GDZ NAD 0.01641 0.42837 10.1852
173 3MCT SAH 0.01203 0.4236 10.1852
174 4MZ7 DTP 0.02995 0.41513 10.1852
175 1T0S BML 0.001019 0.43818 10.4651
176 3CQD ATP 0.006759 0.45595 10.6481
177 3W54 RNB 0.002859 0.44351 10.6481
178 1LC8 33P 0.01175 0.43173 10.6481
179 1SG4 CO8 0.02016 0.42004 10.6481
180 4RNX FMN 0.0174 0.41497 10.6481
181 1FIQ SAL 0.04411 0.40877 10.6481
182 1H16 COA 0.004002 0.44497 11.1111
183 3BS8 PMP 0.01059 0.41449 11.1111
184 3MBG FAD 0.004763 0.44974 11.5741
185 1BUC CAA 0.004622 0.44883 11.5741
186 1BUC FAD 0.0163 0.43419 11.5741
187 3IL6 B83 0.01919 0.41206 11.5741
188 1Y52 BTN 0.01165 0.44766 11.9048
189 1S2D ADE 0.0009519 0.46596 11.976
190 1FP2 HMO 0.01555 0.41091 12.037
191 1F3F D4D 0.04221 0.41382 12.2581
192 3KMZ EQO 0.008553 0.4386 12.5
193 4G1V FAD 0.03607 0.40862 12.5
194 3MPI GRA 0.04489 0.44269 12.963
195 3MPI FAD 0.01137 0.44223 12.963
196 4C0X FMN 0.006403 0.44485 13.4259
197 4C0X AQN 0.02049 0.42468 13.4259
198 3S9K CIT 0.01038 0.41187 14.4068
199 1JYQ MAZ PTR PTM ASN 0.04891 0.42107 14.5833
200 3PVT 3HC 0.02701 0.42488 15.7407
201 1GPJ CIT 0.008413 0.40538 17.5926
202 1WGC SIA GAL BGC 0.004025 0.42895 18.1287
203 2PWY SAH 0.02416 0.41191 18.5185
204 3O55 FAD 0.004117 0.45286 20
205 1ZGA SAH 0.00168 0.45437 20.3704
206 1ZGA HMK 0.002443 0.44428 20.3704
207 3CEV ARG 0.008796 0.41333 22.2222
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