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Receptor
PDB id Resolution Class Description Source Keywords
5MTE 1.4 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF PDF FROM THE VIBRIO PARAHAEMOLYTICUS BACTERIOPHAGE VP16T IN COMPLEX WITH ACTINONIN - CRYSTAL FOR VIBRIO PHAGE VP16T PDF PEPTIDE DEFORMYLASE TYPE 1B BACTERIOPHAGE VP16T ACTIHYDROLASE
Ref.: PEPTIDE DEFORMYLASES FROM VIBRIO PARAHAEMOLYTICUS P BACTERIA DISPLAY SIMILAR DEFORMYLASE ACTIVITY AND I BINDING CLEFTS. BIOCHIM. BIOPHYS. ACTA V.1866 348 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI B:204;
A:203;
B:203;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
58.693 Ni [Ni+2...
BB2 A:201;
B:201;
Valid;
Valid;
none;
none;
submit data
385.498 C19 H35 N3 O5 CCCCC...
ZN B:202;
A:202;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5MTE 1.4 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF PDF FROM THE VIBRIO PARAHAEMOLYTICUS BACTERIOPHAGE VP16T IN COMPLEX WITH ACTINONIN - CRYSTAL FOR VIBRIO PHAGE VP16T PDF PEPTIDE DEFORMYLASE TYPE 1B BACTERIOPHAGE VP16T ACTIHYDROLASE
Ref.: PEPTIDE DEFORMYLASES FROM VIBRIO PARAHAEMOLYTICUS P BACTERIA DISPLAY SIMILAR DEFORMYLASE ACTIVITY AND I BINDING CLEFTS. BIOCHIM. BIOPHYS. ACTA V.1866 348 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5MTE - BB2 C19 H35 N3 O5 CCCCC[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 1205 families.
1 5MTE - BB2 C19 H35 N3 O5 CCCCC[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 1039 families.
1 5MTE - BB2 C19 H35 N3 O5 CCCCC[C@H]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BB2; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 BB2 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5MTE; Ligand: BB2; Similar sites found with APoc: 356
This union binding pocket(no: 1) in the query (biounit: 5mte.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1YP1 LYS ASN LEU None
2 1ZVX FIN None
3 1KUK PCA LYS TRP None
4 1NU4 MLA None
5 1UO4 PIH None
6 5CHR 4NC None
7 4ZGM 32M None
8 5MT9 SRO None
9 2O4N TPV None
10 1MID LAP None
11 3V66 D3A None
12 1UO5 PIH None
13 1N8V BDD None
14 3KP6 SAL None
15 1SBR VIB None
16 6FX2 FUC C4W NAG BMA MAN NAG GAL None
17 5D9J 0N8 None
18 3ND6 ATP None
19 3MWS 017 None
20 4Q5M ROC None
21 1UVC STE None
22 2FP2 TSA None
23 3F8C HT1 None
24 4IGH ORO 1.45985
25 4IGH 1EA 1.45985
26 4IGH FMN 1.45985
27 3C88 ARG ARG GLY CYS NH2 1.45985
28 2CND FAD 1.45985
29 2V57 PRL 1.57895
30 1IDA 0PO 2.0202
31 3N7S 3N7 2.08333
32 4DD8 BAT 2.18978
33 1RM8 BAT 2.18978
34 4ORM FMN 2.18978
35 4ORM 2V6 2.18978
36 4ORM ORO 2.18978
37 4RFM 3P6 2.18978
38 3PE2 E1B 2.18978
39 3SQP 3J8 2.18978
40 1YOK P6L 2.18978
41 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 2.18978
42 6BYM HC3 2.18978
43 5YWX GSH 2.18978
44 5YWX 93C 2.18978
45 2UW1 GVM 2.18978
46 3NFD COA 2.18978
47 5UC1 486 2.18978
48 3QLM PLM 2.41935
49 1R6N 434 2.91971
50 4OHU 2TK 2.91971
51 4OHU NAD 2.91971
52 2GBB CIT 2.91971
53 3EE4 MYR 2.91971
54 3ZZH NLG 2.91971
55 6D6L FY4 2.91971
56 3TWO NDP 2.91971
57 2GWH PCI 3.64964
58 3WV1 WHH 3.64964
59 5O7E 9NB 3.64964
60 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 3.64964
61 1XON PIL 3.64964
62 2YB9 HA0 3.64964
63 4BXK 1IU 3.64964
64 2Z9I GLY ALA THR VAL 3.64964
65 3G58 988 3.64964
66 3X1M COA 3.64964
67 3G4G D71 3.64964
68 6DQU GLY ILE ILE ASN THR LEU 3.64964
69 5C1M OLC 3.64964
70 3AI3 SOE 3.64964
71 2D5Z L35 3.64964
72 1VLH PNS 3.64964
73 2ED4 FAD 3.64964
74 5IM3 DTP 3.64964
75 2D5X L35 3.64964
76 5OLK DTP 3.64964
77 3CEV ARG 3.64964
78 2ZWI C5P 3.64964
79 2AMV BIN 3.64964
80 5B4B LP5 3.64964
81 5O0B 9FE 3.64964
82 4Q9M FPP 3.64964
83 4B52 RDF 3.64964
84 3QFA FAD 4.23892
85 1FBL HTA 4.37956
86 4DV8 0LX 4.37956
87 1HFS L04 4.37956
88 4MRP GSH 4.37956
89 2IV2 MGD 4.37956
90 4UCC ZKW 4.37956
91 5X80 SAL 4.37956
92 5W7B MYR 4.37956
93 3HP9 CF1 4.37956
94 4M52 FAD 4.37956
95 3KFC 61X 4.37956
96 5NWI TYR PHE SER SEP ASN 4.37956
97 6ESN BWE 4.37956
98 3SP6 IL2 4.37956
99 2ZFU SAH 4.37956
100 1JGS SAL 4.37956
101 4RC8 STE 4.37956
102 6ARJ SAH 4.37956
103 6ARJ BW4 4.37956
104 1K7L 544 4.37956
105 3WQM B29 4.37956
106 4UDB CV7 4.37956
107 5NI5 8YB 4.37956
108 5X8G S0N 4.37956
109 4NE2 SH2 4.37956
110 5L7G 6QE 4.37956
111 3KDU NKS 4.37956
112 5ECP MET 4.37956
113 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 4.37956
114 5ECP ATP 4.37956
115 2A9D MTE 4.37956
116 3FEI CTM 4.37956
117 1YMT DR9 4.37956
118 2A3I C0R 4.37956
119 1VAY AZA 4.37956
120 3ET1 ET1 4.37956
121 4TVD BGC 4.37956
122 3EYA FAD 4.37956
123 1ATL 0QI 5.10949
124 3Q2H QHF 5.10949
125 4IN9 SER TRP PHE PRO 5.10949
126 3B9Z CO2 5.10949
127 5OCA 9QZ 5.10949
128 3ZVS MLI 5.10949
129 5G57 6M5 5.10949
130 4LY9 1YY 5.10949
131 4LY9 S6P 5.10949
132 1J1R ADE 5.10949
133 1UY4 XYP XYP XYP XYP 5.10949
134 3AHO 3A2 5.10949
135 5K53 STE 5.10949
136 3E70 GDP 5.10949
137 4WVH ASP HIS ASP ALA HIS ALA 5.10949
138 4I90 CHT 5.10949
139 2ZWA SAH 5.10949
140 1XOC VAL ASP SER LYS ASN THR SER SER TRP 5.10949
141 2Q8G AZX 5.10949
142 1RJD SAM 5.10949
143 5KD8 TNR 5.10949
144 6GAR FAD 5.10949
145 1SOX MTE 5.10949
146 4WOE 3S5 5.10949
147 4WKI 3PW 5.83942
148 2J83 BAT 5.83942
149 1BKC INN 5.83942
150 2W14 WR2 5.83942
151 1MMQ RRS 5.83942
152 3EWC MCF 5.83942
153 2FV5 541 5.83942
154 1B7H LYS NLE LYS 5.83942
155 5DUF G7A 5.83942
156 6BTN E8M 5.83942
157 6CAY ERG 5.83942
158 3WYJ H78 5.83942
159 2YJD YJD 5.83942
160 6GL8 F3Q 5.83942
161 3COW 52H 5.83942
162 6F5W KG1 5.83942
163 4JDR FAD 5.83942
164 1BZL FAD 5.83942
165 2V5E SCR 5.94059
166 3R1V AZB 6.29921
167 1Q3A NGH 6.56934
168 1R55 097 6.56934
169 2VJ8 HA2 6.56934
170 4GAA BES 6.56934
171 4WGF HX2 6.56934
172 2P4Y C03 6.56934
173 2ZB4 5OP 6.56934
174 2ZB4 NAP 6.56934
175 3SFI 3SF 6.56934
176 2I0G I0G 6.56934
177 5UWA 8ND 6.56934
178 4B7P 9UN 6.56934
179 4WZV E40 6.56934
180 1U3U BNF 6.56934
181 1U3U NAD 6.56934
182 3W2E FAD 6.56934
183 3W2E NAD 6.56934
184 5ZI7 GLU 6.56934
185 3T03 3T0 6.56934
186 3B1M KRC 6.56934
187 4COL DTP 6.56934
188 2OZ5 7XY 6.56934
189 1FIQ FAD 6.56934
190 2HFP NSI 6.56934
191 5EY0 GTP 6.56934
192 2BTM PGA 6.56934
193 3KC1 2T6 7.12166
194 2ZXG S23 7.29927
195 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 7.29927
196 4QHP 32Q 7.29927
197 2BCG GER 7.29927
198 6BA2 7KM 7.29927
199 1ZPD CIT 7.29927
200 1KQF MGD 7.29927
201 6F6E PLM 7.29927
202 1LLF F23 7.29927
203 1SQL GUN 7.29927
204 5JO1 6LM 7.29927
205 3IPQ 965 8
206 4AIG FLX 8.0292
207 5UGW GSH 8.0292
208 4AR8 IP8 GLY PRO ALA 8.0292
209 4OGQ 7PH 8.0292
210 4CA5 3EF 8.0292
211 4OGQ 2WD 8.0292
212 4PGK Y69 8.0292
213 5C2H 4XU 8.0292
214 5C2H 4PX 8.0292
215 5CX6 CDP 8.0292
216 3WCA FPS 8.0292
217 5AZC PGT 8.0292
218 3RMK BML 8.0292
219 2RCU BUJ 8.0292
220 4YMX ARG 8.0292
221 3D04 SAK 8.0292
222 1QM5 PLP 8.0292
223 2GJN NIS 8.0292
224 4OGQ 1O2 8.0292
225 5M36 9SZ 8.75912
226 2DM6 IMN 8.75912
227 2DM6 NAP 8.75912
228 2AX9 BHM 8.75912
229 5M37 9SZ 8.75912
230 4E2J MOF 8.75912
231 4KP7 1UQ 8.75912
232 4KP7 NAP 8.75912
233 2JC9 ADN 8.75912
234 5UFS 1TA 8.75912
235 1FEC FAD 8.75912
236 4TMN 0PK 8.75912
237 3WQQ IB3 8.75912
238 3WQQ NDP 8.75912
239 4F4S EFO 9.21053
240 5OHJ 9VE 9.48905
241 3GWT 066 9.48905
242 2ZCQ B65 9.48905
243 1SR7 MOF 9.48905
244 1NF8 BOG 9.48905
245 1XMY ROL 9.48905
246 1XM4 PIL 9.48905
247 4C3Y FAD 9.48905
248 4OAR 2S0 9.48905
249 1XMU ROF 9.48905
250 3AB1 FAD 9.48905
251 3CXH SMA 9.48905
252 1PS9 FAD 9.48905
253 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 10.219
254 3GZ9 D32 10.219
255 3LDW ZOL 10.219
256 5EK3 5PK 10.219
257 4YSX FAD 10.219
258 2Q1H AS4 10.219
259 4DJA FAD 10.219
260 4DJA DLZ 10.219
261 6MVU K4V 10.219
262 4B6C B5U 10.219
263 3W54 RNB 10.219
264 3UG4 AHR 10.219
265 1Q7E MET 10.9489
266 4WO4 JLS 10.9489
267 6C1R EFD 10.9489
268 6BMN PAP 10.9489
269 3RUG DB6 10.9489
270 1E1M NAP 10.9489
271 1E1M FAD 10.9489
272 1RM6 FAD 10.9489
273 4QOM PYG 10.9489
274 1XDY MTE 10.9489
275 5TO8 7FM 10.9489
276 4P6X HCY 11.6788
277 4KWD JF2 11.6788
278 2CUN 3PG 11.6788
279 2YPI PGA 11.6788
280 3BQD DAY 11.6788
281 1NHZ 486 11.6788
282 3GGU 017 12.1212
283 2E2R 2OH 12.4088
284 3OKI OKI 12.4088
285 3DWB RDF 12.4088
286 5ME4 HP4 12.4088
287 1UWK URO 12.4088
288 1UWK NAD 12.4088
289 2YIV YIV 12.4088
290 1POC GEL 12.6866
291 5LX9 OLB 13.1387
292 4RW3 TDA 13.1387
293 5LWY OLB 13.1387
294 5LWY OLA 13.1387
295 4ZW3 4S9 13.8686
296 3HBV ALA LYS ALA SER GLN ALA ALA 13.8686
297 1EU1 GLC 13.8686
298 5Y02 HBX 14.0187
299 1CMC SAM 14.4231
300 3AKI AH8 14.5985
301 1V97 MTE 14.5985
302 5FVJ ACO 15.3285
303 2IDO TMP 15.6627
304 5TCI 79V 16.0584
305 1ZED PNP 16.0584
306 1T0S BML 16.0584
307 2TCL RO4 16.7883
308 3H0A D30 16.7883
309 1RDT L79 16.7883
310 2BJ4 OHT 16.7883
311 1DKF OLA 16.7883
312 4POJ 2VP 16.7883
313 4M8E 29V 16.7883
314 3FAL LO2 16.7883
315 1FM9 9CR 16.7883
316 3H0A 9RA 16.7883
317 3FAL REA 16.7883
318 6A5Y 9CR 16.7883
319 1MJT ITU 16.7883
320 4KX8 L2O VAL VAL ASP 17.5182
321 4MGA 27L 17.5182
322 2QE4 JJ3 17.5182
323 5AAV GW5 17.5182
324 4MGB XDH 17.5182
325 4TV1 36M 17.5182
326 1MT1 AG2 17.6991
327 1XVB BHL 18.2482
328 1R5L VIV 18.2482
329 5Z84 CHD 18.3673
330 5ZCO CHD 18.3673
331 5W97 CHD 18.3673
332 5ZCO PGV 18.3673
333 2DYS PGV 18.3673
334 5Z84 PGV 18.3673
335 2DYR PEK 18.3673
336 2DYR PGV 18.3673
337 2DYS PEK 18.3673
338 3TGE TGE 19.708
339 5K52 OCD 21.1679
340 1N13 AG2 21.2389
341 2QQD AG2 21.4286
342 2QQC AG2 21.4286
343 2Y69 CHD 21.7054
344 2OUA AES 24.8175
345 5DK4 5BX 30.6569
346 5DK4 ATP 30.6569
347 5G3N X28 32.2835
348 1M2Z BOG 38.0952
349 3GN8 DEX 38.0952
350 2OKL BB2 40.8759
351 1WS1 BB2 42.3358
352 3M6P BB2 44.5255
353 3G5K BB2 44.5255
354 1G27 BB1 44.5255
355 4DR9 BB2 47.4453
356 3E3U NVC 47.4453
Pocket No.: 2; Query (leader) PDB : 5MTE; Ligand: BB2; Similar sites found with APoc: 75
This union binding pocket(no: 2) in the query (biounit: 5mte.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 3K1X DBX None
2 4P6G 2FZ None
3 2P0D I3P None
4 1ZEI CRS None
5 2UZH IPE None
6 3RET SAL None
7 3RET PYR None
8 1TL2 NDG 1.45985
9 6FA4 D1W 1.45985
10 4F8L AES 2.91971
11 5F1R 42O 2.91971
12 3TL1 JRO 2.91971
13 4OEV OXL 2.91971
14 1TE2 PGA 3.64964
15 1T27 PCW 3.64964
16 1NAA 6FA 3.64964
17 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 3.80952
18 2A8X FAD 4.37956
19 3GF2 SAL 4.37956
20 1GJW GLC 4.37956
21 1YXM ADE 4.37956
22 6CS8 F9Y 4.37956
23 4BNU 9KQ 4.37956
24 4YDD MGD 5.10949
25 4YDD MD1 5.10949
26 1SB8 NAD 5.10949
27 1SB8 UD2 5.10949
28 5WBF LAC 5.10949
29 3ZUY TCH 5.10949
30 6BWL NAD 5.10949
31 4UBS DIF 5.10949
32 3LU1 NAD 5.10949
33 2IDV M7G 5.10949
34 5H20 GLC 5.40541
35 5ZRR 9J3 5.83942
36 4C2C ALA ALA ALA 5.83942
37 2CWH PYC 5.83942
38 4NTD FAD 5.83942
39 4C2G ALA ALA ALA ALA 5.83942
40 2FXD DR7 6.06061
41 3TDC 0EU 6.56934
42 5AE2 FAD 6.56934
43 1UDB NAD 6.56934
44 1UDB UFG 6.56934
45 1RZM E4P 7.29927
46 3EWP APR 7.29927
47 4G31 0WH 7.29927
48 1OUK 084 8.0292
49 5C9P FUC 8.0292
50 2Y7P SAL 8.0292
51 4WZ8 3W7 8.0292
52 2PZM NAD 8.0292
53 2PZM UDP 8.0292
54 2P3C 3TL 8.08081
55 4J56 FAD 8.75912
56 2WMC MGP 9.48905
57 1EZV SMA 9.48905
58 3PVT 3HC 10.219
59 4ZOH FAD 10.9489
60 4OIV XX9 11.6788
61 1C1X HFA 11.6788
62 1R6D NAD 12.4088
63 4OYA 1VE 13.1387
64 5EEH P9P 13.1387
65 5LGA 6VH 14.5985
66 5OJI ISN 14.5985
67 4URX FK1 15.3285
68 6BVM EBV 15.3285
69 6BVJ EAS 15.3285
70 6BVK EAV 15.3285
71 6BVL EBY 15.3285
72 6BVI EC4 15.3285
73 3CHT 4NB 16.0584
74 4MG9 27K 17.5182
75 5ZCO PEK 18.3673
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