Receptor
PDB id Resolution Class Description Source Keywords
4OHB 2.4 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF MILB E103A IN COMPLEX WITH 5- HYDROXYMETHYLCYTIDINE 5'-MONOPHOSPHATE (HMCMP) FROM STREPTOR IMOFACIENS STREPTOMYCES RIMOFACIENS HYDROLASE PROTEIN-HMCMP COMPLEX
Ref.: STRUCTURE OF THE N-GLYCOSIDASE MILB IN COMPLEX WITH HYDROXYMETHYL CMP REVEALS ITS ARG23 SPECIFICALLY RE THE SUBSTRATE AND CONTROLS ITS ENTRY NUCLEIC ACIDS RES. V. 42 8115 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5HM A:201;
Valid;
none;
submit data
353.223 C10 H16 N3 O9 P C1=C(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4OHB 2.4 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF MILB E103A IN COMPLEX WITH 5- HYDROXYMETHYLCYTIDINE 5'-MONOPHOSPHATE (HMCMP) FROM STREPTOR IMOFACIENS STREPTOMYCES RIMOFACIENS HYDROLASE PROTEIN-HMCMP COMPLEX
Ref.: STRUCTURE OF THE N-GLYCOSIDASE MILB IN COMPLEX WITH HYDROXYMETHYL CMP REVEALS ITS ARG23 SPECIFICALLY RE THE SUBSTRATE AND CONTROLS ITS ENTRY NUCLEIC ACIDS RES. V. 42 8115 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 4OHB - 5HM C10 H16 N3 O9 P C1=C(C(=NC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 176 families.
1 4OHB - 5HM C10 H16 N3 O9 P C1=C(C(=NC....
2 4JEM - C5P C9 H14 N3 O8 P C1=CN(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 143 families.
1 4OHB - 5HM C10 H16 N3 O9 P C1=C(C(=NC....
2 4JEM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5HM; Similar ligands found: 26
No: Ligand ECFP6 Tc MDL keys Tc
1 5HM 1 1
2 TKW 0.681159 0.958333
3 CAR 0.575342 0.944444
4 C 0.575342 0.944444
5 C5P 0.575342 0.944444
6 16B 0.519481 0.881579
7 5FU 0.480519 0.855263
8 CDP 0.47561 0.958333
9 CNU 0.469136 0.917808
10 ICR 0.468354 0.84
11 5BU 0.468354 0.855263
12 U5P 0.467532 0.888889
13 F01 0.465753 0.815789
14 CTP 0.458824 0.958333
15 7XL 0.454545 0.932432
16 JW5 0.432099 0.90411
17 C2G 0.423913 0.945205
18 NUP 0.419753 0.931507
19 CDP MG 0.418605 0.868421
20 UP6 0.4125 0.84
21 C5G 0.412371 0.932432
22 5AE 0.405405 0.794521
23 BMQ 0.405063 0.837838
24 8OP 0.404494 0.810127
25 CDM 0.402062 0.884615
26 H2U 0.4 0.815789
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4OHB; Ligand: 5HM; Similar sites found: 240
This union binding pocket(no: 1) in the query (biounit: 4ohb.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1M5B BN1 0.0008328 0.46341 None
2 1UO5 PIH 0.0111 0.44168 None
3 2E1A MSE 0.001191 0.42911 None
4 1I0Z OXM 0.03084 0.40281 None
5 3TA2 ATP 0.00879 0.40215 None
6 3IL6 B83 0.003149 0.40033 None
7 1BTN I3P 0.03713 0.41546 0.943396
8 9LDT NAD 0.00172 0.42606 1.05263
9 1VQ2 DDN 0.03094 0.40115 1.05263
10 1V35 NAI 0.01467 0.40111 1.57895
11 2Q37 3AL 0.001374 0.43873 1.65746
12 1QJC PNS 0.02024 0.4039 1.89873
13 1YOA FMN 0.0004653 0.51643 2.10526
14 1BGQ RDC 0.001709 0.42033 2.10526
15 1AX2 NDG GAL 0.00008704 0.41324 2.10526
16 4JK3 NAD 0.006123 0.40253 2.10526
17 4GYW UDP 0.004061 0.41319 2.213
18 3F8C HT1 0.004544 0.41679 2.38095
19 4IZC 1GZ 0.004088 0.42988 2.63158
20 2C5S AMP 0.002184 0.41872 2.63158
21 4LSJ LSJ 0.001674 0.41207 2.63158
22 1NHZ 486 0.002347 0.40862 2.63158
23 1ECM TSA 0.0003635 0.44944 2.75229
24 2Q8H TF4 0.004223 0.44568 3.15789
25 1TDF FAD 0.002883 0.43382 3.15789
26 1TDF NAP 0.006752 0.43382 3.15789
27 4CS4 AXZ 0.002641 0.43254 3.15789
28 4CS4 ANP 0.002301 0.42864 3.15789
29 1H82 FAD 0.006346 0.42713 3.15789
30 1H82 GZZ 0.007132 0.42713 3.15789
31 1B9I PXG 0.001067 0.42284 3.15789
32 2Q09 DI6 0.002945 0.41359 3.15789
33 3PFG SAM 0.00835 0.40985 3.15789
34 3PFG TLO 0.00835 0.40985 3.15789
35 3CQD ATP 0.009213 0.40517 3.15789
36 1FL2 FAD 0.01161 0.40421 3.15789
37 1LVL FAD 0.01362 0.40417 3.15789
38 1RZM PEP 0.007712 0.40189 3.15789
39 1L1Q 9DA 0.001257 0.41458 3.22581
40 3F81 STT 0.003873 0.44753 3.27869
41 3QDT A2G GAL 0.002419 0.44924 3.4965
42 4K7O EKZ 0.0282 0.40282 3.57143
43 1G8S MET 0.0006948 0.45844 3.68421
44 1KBJ FMN 0.000274 0.44808 3.68421
45 4M5P MLA 0.005991 0.44664 3.68421
46 1KBI FMN 0.0003372 0.44649 3.68421
47 1KBI PYR 0.0003372 0.44649 3.68421
48 2EB5 OXL 0.001727 0.44114 3.68421
49 1Q7E MET 0.001021 0.42864 3.68421
50 3MAG 3MA 0.01541 0.42537 3.68421
51 1C0I FAD 0.004938 0.42356 3.68421
52 1C0I BE2 0.004938 0.42356 3.68421
53 2YVF FAD 0.009869 0.42127 3.68421
54 2YVF NAD 0.01024 0.42127 3.68421
55 3ZPG 5GP 0.01627 0.41666 3.68421
56 4CKU P2F 0.00916 0.41448 3.68421
57 4M5P 23W 0.01318 0.41433 3.68421
58 4DQ2 BTX 0.003258 0.41283 3.68421
59 1R37 NAD 0.005017 0.41209 3.68421
60 2BJK NAD 0.0152 0.409 3.68421
61 3UXL CFI 0.01066 0.4066 3.68421
62 2BKA NDP 0.00594 0.40303 3.68421
63 4LHM AZZ 0.01109 0.40037 3.68421
64 1KGQ NPI 0.04488 0.40003 4.0146
65 1KGQ SCO 0.04668 0.40003 4.0146
66 2WGC SIA GAL BGC 0.04943 0.40608 4.09357
67 1Y9Q MED 0.004982 0.42098 4.16667
68 2C7G FAD 0.004323 0.43325 4.21053
69 1QDS PGA 0.0007788 0.43064 4.21053
70 2C7G ODP 0.004959 0.43005 4.21053
71 1N1G BCP 0.001996 0.4287 4.21053
72 4DEM YS4 0.01888 0.41905 4.21053
73 3LTW HLZ 0.007274 0.41377 4.21053
74 4USQ FAD 0.006181 0.40861 4.21053
75 1WNG SAH 0.002328 0.40502 4.21053
76 4G1V FAD 0.004767 0.40379 4.21053
77 1JUV NDP 0.004966 0.40313 4.21053
78 2X61 NGA GAL SIA 0.02478 0.40266 4.21053
79 3BS8 PMP 0.001038 0.40181 4.21053
80 2YBQ UP2 0.01058 0.40178 4.21053
81 3DCM SAM 0.00288 0.40171 4.21053
82 2IMP NAI 0.04735 0.40073 4.21053
83 3A1I UNU 0.00047 0.43901 4.73684
84 1GEX PLP HSA 0.001042 0.42667 4.73684
85 1LDM NAD 0.01471 0.41595 4.73684
86 2YYJ 4HP 0.03734 0.40618 4.73684
87 2YYJ FAD 0.03734 0.40618 4.73684
88 1FA2 DOM 0.004963 0.40596 4.73684
89 1OAA OAA 0.01302 0.40496 4.73684
90 1YS4 NAP 0.003494 0.40235 4.73684
91 1ZK7 FAD 0.01796 0.40104 4.73684
92 2IYG FMN 0.001556 0.4141 4.83871
93 4NAT ADP 0.03309 0.40847 5
94 2BNE U5P 0.0009887 0.43855 5.26316
95 1WDA BAG 0.0009264 0.43341 5.26316
96 3T31 DCQ 0.006906 0.42561 5.26316
97 3T31 FAD 0.006429 0.42543 5.26316
98 1PEA ACM 0.007948 0.42476 5.26316
99 3P7I P7I 0.002373 0.4228 5.26316
100 1QD0 RR6 0.00092 0.42255 5.26316
101 1Z42 FMN 0.0003611 0.41591 5.26316
102 1V9N NDP 0.003448 0.41589 5.26316
103 3PY5 AMP 0.001621 0.40422 5.26316
104 4W97 UCA 0.004377 0.40211 5.26316
105 3UEC ALA ARG TPO LYS 0.007255 0.41994 5.47945
106 4KCF FMN 0.000645 0.40704 5.50661
107 3ZZL TRP 0.01047 0.40501 5.71429
108 1VDC FAD 0.0003892 0.46969 5.78947
109 4COQ SAN 0.00119 0.44821 5.78947
110 2Y7P SAL 0.002511 0.4218 5.78947
111 3LZW FAD 0.003998 0.42038 5.78947
112 1RYI GOA 0.005635 0.41945 5.78947
113 1NZY BCA 0.002539 0.41545 5.78947
114 1UXG FUM 0.00608 0.41326 5.78947
115 1UXG NAD 0.00608 0.41326 5.78947
116 3LZW NAP 0.0173 0.4098 5.78947
117 4O1M NAD 0.005233 0.40644 5.78947
118 1RYI FAD 0.01139 0.40547 5.78947
119 2PTZ PAH 0.00151 0.40529 5.78947
120 3FPZ AHZ 0.039 0.4044 5.78947
121 4ARF IP8 GLY PRO ALA 0.001652 0.40393 5.78947
122 1RP0 AHZ 0.03268 0.4036 5.78947
123 1OFD FMN 0.02673 0.40072 5.78947
124 2OYS FMN 0.001129 0.41822 6.19835
125 1T0S BML 0.0007712 0.47273 6.31579
126 1EP2 ORO 0.002787 0.42191 6.31579
127 1T0I FMN 0.001622 0.40859 6.31579
128 2AQJ FAD 0.02145 0.40657 6.31579
129 2AQJ TRP 0.02187 0.40557 6.31579
130 2J8Z NAP 0.005648 0.40385 6.31579
131 1EP2 FMN 0.005386 0.40324 6.31579
132 1GV0 NAD 0.006605 0.40261 6.31579
133 3TKA SAM 0.003105 0.40242 6.31579
134 4AF0 IMP 0.01836 0.40226 6.31579
135 4KCT FDP 0.003596 0.40062 6.31579
136 2F2U M77 0.002018 0.41484 6.46766
137 1MDZ DCS 0.001785 0.42808 6.84211
138 4C12 ADP 0.007436 0.42133 6.84211
139 1D6H COA 0.005489 0.41991 6.84211
140 1KOL NAD 0.004011 0.41814 6.84211
141 1X54 4AD 0.002095 0.41386 6.84211
142 1TIW FAD 0.008169 0.40824 6.84211
143 1TIW TFB 0.008169 0.40824 6.84211
144 2XDQ MGX 0.03124 0.40253 6.84211
145 2XK9 XK9 0.009332 0.40172 6.84211
146 4O8A FAD 0.00796 0.40081 6.84211
147 2V5E SCR 0.01916 0.42045 6.93069
148 1S2D ADE 0.0001524 0.46974 7.18563
149 3R35 4CO 0.005243 0.4077 7.28477
150 3O7B SAH 0.0003222 0.43347 7.36842
151 4PLG NAI 0.004152 0.41866 7.36842
152 4PLG OXM 0.004152 0.41866 7.36842
153 2NLI LAC 0.01376 0.41461 7.36842
154 2NLI FMN 0.01276 0.41461 7.36842
155 1V6A TRE 0.005116 0.41461 7.36842
156 1JA9 PYQ 0.003871 0.41002 7.36842
157 2NX1 PEP 0.004067 0.4078 7.36842
158 2NX1 RP5 0.004438 0.40639 7.36842
159 1UF5 CDT 0.003205 0.40716 7.59076
160 3RF4 FUN 0.006548 0.40479 7.75862
161 2IZ1 ATR 0.0006679 0.4592 7.89474
162 3Q9T FAY 0.0004377 0.45787 7.89474
163 3F3E LEU 0.001411 0.43689 7.89474
164 2V6O FAD 0.008421 0.43091 7.89474
165 1YBH FAD 0.002641 0.42848 7.89474
166 1Q8S MAN MMA 0.01076 0.41882 7.89474
167 1Q8Q MAN MMA 0.01104 0.41816 7.89474
168 2GND MAN 0.01363 0.41299 7.89474
169 3PC3 P1T 0.001778 0.41114 7.89474
170 2R40 20E 0.002808 0.40919 7.89474
171 1DR1 HBI 0.002197 0.42942 7.93651
172 1DR1 NAP 0.002197 0.42942 7.93651
173 4RJK PYR 0.0009252 0.46899 8.42105
174 3OND NAD 0.00258 0.43665 8.42105
175 3OND ADN 0.00258 0.43665 8.42105
176 2WUF KEM 0.0008294 0.42684 8.42105
177 2Q2V NAD 0.002116 0.42264 8.42105
178 4FWE FAD 0.007471 0.41458 8.42105
179 1BDB NAD 0.02145 0.4125 8.42105
180 1DLJ NAI 0.01336 0.40943 8.42105
181 1GS5 NLG 0.005956 0.40805 8.42105
182 1GS5 ANP 0.005956 0.40805 8.42105
183 1DLJ UGA 0.01682 0.40535 8.42105
184 1T10 F6P 0.009897 0.40247 8.42105
185 4J7H TRH 0.002861 0.40182 8.42105
186 1V7R CIT 0.01582 0.42478 8.60215
187 3H86 AP5 0.005861 0.42593 8.94737
188 2NCD ADP 0.003052 0.42409 8.94737
189 3PNL ADP 0.001587 0.41477 8.94737
190 1SS4 CIT 0.0008359 0.51322 9.15033
191 1SS4 GSH 0.006154 0.4645 9.15033
192 2ZWS PLM 0.00431 0.46402 9.47368
193 3BW2 FMN 0.001118 0.43173 9.47368
194 2JFV FLC 0.007169 0.41404 9.47368
195 3D3W NAP 0.004161 0.41151 9.47368
196 3KJQ B94 0.002745 0.40497 9.7561
197 1JQI FAD 0.00009479 0.4811 10
198 3I0O SMI 0.001718 0.43464 10
199 4HA6 FAD 0.003933 0.42567 10
200 1GR0 NAD 0.03042 0.40707 10
201 1XX4 BAM 0.03319 0.40121 10
202 2Q97 ATP 0.0002689 0.44269 10.5263
203 4DYO SD4 0.003347 0.4114 10.5263
204 4JWX 1N4 0.006172 0.40584 10.5263
205 2BGM NAJ 0.02498 0.40251 10.5263
206 1O51 ADP 0.0048 0.40218 10.5263
207 1ZGS XMM 0.02096 0.40206 10.5263
208 2ZJ3 G6P 0.002287 0.40529 11.0526
209 2NXW TPP 0.007678 0.40263 11.0526
210 3FC4 EDO 0.01541 0.40911 11.5789
211 2C31 ADP 0.008763 0.42902 12.1053
212 2C31 TZD 0.012 0.4238 12.1053
213 1CSI CMX 0.004363 0.41994 12.1053
214 1CSI OAA 0.004363 0.41994 12.1053
215 2P1O IHP 0.003813 0.41163 12.1053
216 2P1O NLA 0.003813 0.41163 12.1053
217 2QCX PF1 0.00386 0.41978 12.6316
218 4KXV TDP DX5 0.005998 0.41349 13.1579
219 4C25 13P 0.003708 0.41072 13.1579
220 4F4S EFO 0.005544 0.40775 13.1579
221 2XBP ATP 0.006751 0.41855 13.2743
222 1ULE GLA GAL NAG 0.00364 0.44084 13.3333
223 1RYD NDP 0.009262 0.40508 13.6842
224 4K5S FAD 0.007474 0.40427 14.2105
225 4K5S PM0 0.01712 0.40427 14.2105
226 3S9K CIT 0.0003804 0.51641 14.4068
227 2PT9 2MH 0.008641 0.403 14.7368
228 2PT9 S4M 0.005024 0.40145 14.7368
229 2YHW BM3 0.001086 0.43219 15.2632
230 4AT0 FAD 0.005101 0.42473 15.2632
231 2Q28 TPP 0.001253 0.42372 15.2632
232 4R33 TRP 0.003345 0.41765 15.2632
233 4R33 SAH 0.003345 0.41765 15.2632
234 2F01 BTQ 0.01797 0.4129 17.3228
235 1HFS L04 0.004196 0.41264 17.5
236 1TUV VK3 0.03221 0.40186 17.5439
237 1EXB NDP 0.01402 0.42036 21.3592
238 1EZV SMA 0.001786 0.41963 21.5789
239 2XBN PMP 0.003039 0.40952 21.5789
240 4P5E N6P 0.00001311 0.52689 23.0263
Pocket No.: 2; Query (leader) PDB : 4OHB; Ligand: 5HM; Similar sites found: 36
This union binding pocket(no: 2) in the query (biounit: 4ohb.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JBW TMF 0.0355 0.40244 1.57895
2 1ZUA NAP 0.03254 0.42048 2.63158
3 1ZUA TOL 0.03254 0.42048 2.63158
4 4O4K 2PK 0.01562 0.40757 2.63158
5 4CZG ADP 0.03008 0.40722 2.63158
6 4CZG QH3 0.03148 0.40722 2.63158
7 3VC3 C6P 0.02074 0.40589 2.63158
8 4FC7 COA 0.04416 0.40583 2.63158
9 4FC7 NAP 0.04416 0.40583 2.63158
10 1GKZ ADP 0.00952 0.4129 4.21053
11 1G0N PHH 0.02036 0.42282 4.73684
12 1G0N NDP 0.01817 0.42262 4.73684
13 4XP7 FNR 0.01092 0.41002 5.20231
14 3EXS 5RP 0.009207 0.40289 5.26316
15 1OFD AKG 0.01372 0.42373 5.78947
16 1MJH ATP 0.01086 0.41369 6.17284
17 1IV2 CDP 0.007105 0.41288 6.57895
18 2BGS NDP 0.01306 0.42248 6.84211
19 4N02 FNR 0.01244 0.41552 7.36842
20 1JA9 NDP 0.02834 0.40642 7.36842
21 5KOR GDP 0.01663 0.40292 9.47368
22 1YAG ATP 0.007513 0.42484 10
23 5MBX FAD 0.03998 0.41627 10.5263
24 5MBX SP5 0.03998 0.41627 10.5263
25 2GAG FOA 0.03906 0.41109 10.5263
26 4C3Y FAD 0.04844 0.40285 11.0526
27 2FLI DX5 0.01385 0.4068 12.6316
28 1EKO I84 0.03307 0.41337 13.1579
29 1EKO NAP 0.03751 0.40962 13.1579
30 3HGM ATP 0.01139 0.41268 13.6054
31 3ZEI AWH 0.03111 0.40086 13.6842
32 2Q28 ADP 0.02613 0.41881 15.2632
33 4LRZ ADP 0.01083 0.41019 15.7895
34 5TTJ FAD 0.02581 0.41649 18.9474
35 3CR3 ADP 0.005977 0.42268 20
36 5G5G MCN 0.03489 0.40588 35.2632
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