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Receptor
PDB id Resolution Class Description Source Keywords
1Q7E 1.6 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF YFDW PROTEIN FROM E. COLI ESCHERICHIA COLI STRUCTURAL GENOMICS INTERTWINED DIMER PSI PROTEIN STRUCTUINITIATIVE NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENNYSGXRC TRANSFERASE
Ref.: STRUCTURE OF ESCHERICHIA COLI YFDW, A TYPE III COA TRANSFERASE. ACTA CRYSTALLOGR.,SECT.D V. 60 507 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MET A:500;
A:600;
Valid;
Valid;
none;
none;
submit data
149.211 C5 H11 N O2 S CSCC[...
MPD A:1000;
A:1100;
A:1200;
A:1300;
A:700;
A:800;
A:900;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
118.174 C6 H14 O2 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1Q7E 1.6 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF YFDW PROTEIN FROM E. COLI ESCHERICHIA COLI STRUCTURAL GENOMICS INTERTWINED DIMER PSI PROTEIN STRUCTUINITIATIVE NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENNYSGXRC TRANSFERASE
Ref.: STRUCTURE OF ESCHERICHIA COLI YFDW, A TYPE III COA TRANSFERASE. ACTA CRYSTALLOGR.,SECT.D V. 60 507 2004
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 1PT8 - OXL C2 O4 C(=O)(C(=O....
2 1PT5 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 1Q7E - MET C5 H11 N O2 S CSCC[C@@H]....
4 1Q6Y - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 237 families.
1 1PT8 - OXL C2 O4 C(=O)(C(=O....
2 1PT5 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 1Q7E - MET C5 H11 N O2 S CSCC[C@@H]....
4 1Q6Y - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
5 1P5R - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
6 1T3Z - CAO C21 H36 N7 O17 P3 S CC(C)(CO[P....
7 1VGR - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
8 2VJO - OXL C2 O4 C(=O)(C(=O....
9 1VGQ - CAO C21 H36 N7 O17 P3 S CC(C)(CO[P....
10 3UBM - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 1PT8 - OXL C2 O4 C(=O)(C(=O....
2 1PT5 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 1Q7E - MET C5 H11 N O2 S CSCC[C@@H]....
4 1Q6Y - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
5 1P5R - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
6 1T3Z - CAO C21 H36 N7 O17 P3 S CC(C)(CO[P....
7 1VGR - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
8 2VJO - OXL C2 O4 C(=O)(C(=O....
9 1VGQ - CAO C21 H36 N7 O17 P3 S CC(C)(CO[P....
10 3UBM - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MET; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 MED 1 1
2 MET 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 MF3 0.5 0.647059
7 NVA 0.5 0.758621
8 HSE 0.466667 0.617647
9 DAB 0.466667 0.636364
10 MHO 0.457143 0.717949
11 SME 0.457143 0.717949
12 HCS 0.451613 0.733333
13 API 0.451613 0.606061
14 CDT 0.447368 0.756757
15 2MM 0.444444 0.657143
16 NLE 0.441176 0.766667
17 ONL 0.441176 0.71875
18 UN1 0.428571 0.606061
19 11C 0.428571 0.606061
20 MSE 0.428571 0.9
21 DGL 0.424242 0.625
22 GGL 0.424242 0.625
23 GLU 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 FME 0.410256 0.84375
27 AME 0.410256 0.771429
28 LEU 0.40625 0.666667
29 JM6 0.4 0.7
30 CYS 0.4 0.666667
31 DCY 0.4 0.666667
32 C2N 0.4 0.633333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1Q7E; Ligand: MET; Similar sites found with APoc: 369
This union binding pocket(no: 1) in the query (biounit: 1q7e.bio1) has 6 residues
No: Leader PDB Ligand Sequence Similarity
1 4F4S EFO None
2 1FK5 OLA None
3 3D78 NBB None
4 2ZFZ ARG None
5 4I67 G G G RPC None
6 1UO5 PIH None
7 5TVI O8N None
8 5ZKC 3C0 0.950119
9 5DF1 NAP 1.3587
10 5DF1 58X 1.3587
11 3ET1 ET1 1.37457
12 1RQJ RIS 1.40187
13 1TIW FAD 1.40187
14 1TIW TFB 1.40187
15 3SP6 IL2 1.40351
16 4F4P 0SB 1.4652
17 4E2J MOF 1.6
18 3GN8 DEX 1.60643
19 5UFS 1TA 1.6129
20 2Q2Y ADP 1.63488
21 2Q2Y MKR 1.63488
22 4QO5 NAG 1.63551
23 2P4Q FLC 1.63551
24 4ASJ N6A 1.70648
25 2C9E PID 1.83486
26 1ZED PNP 1.8595
27 2W90 6PG 1.86916
28 5CX8 TG6 1.86916
29 3G4G D71 1.90024
30 4Q0P 0MK 1.92308
31 4JZX 476 1.9337
32 3BJC WAN 1.93622
33 5BVE 4VG 1.93906
34 2E3N 6CM 1.96078
35 1P1M MET 1.97044
36 5DRB 5FJ 2.06186
37 5DCH 1YO 2.08333
38 5KOR GDP 2.1028
39 3F5K CE5 2.1028
40 3IQE F42 2.12014
41 3IQE H4M 2.12014
42 4LH7 NMN 2.16718
43 3WCA FPS 2.19178
44 6D28 NEC 2.1978
45 1N83 CLR 2.22222
46 3I51 6PL 2.22222
47 4KWD JF2 2.2293
48 5N9T 8QQ 2.2409
49 3KMZ EQO 2.25564
50 3KMR EQN 2.25564
51 4XDA ADP 2.26537
52 4XDA RIB 2.26537
53 5WGD EST 2.29885
54 5WGQ EST 2.29885
55 5DX3 EST 2.29885
56 5DXE EST 2.29885
57 5DXG EST 2.29885
58 5HYR EST 2.32558
59 2QA8 GEN 2.32558
60 2QZO KN1 2.32558
61 4JKV 1KS 2.33645
62 4NB5 2JT 2.33918
63 4TUZ 36J 2.35294
64 4MG8 27J 2.35294
65 4MG9 27K 2.35294
66 4MGA 27L 2.35294
67 4MG7 27H 2.35294
68 4MGD 27N 2.35294
69 4MGB XDH 2.35294
70 5OHJ 9VE 2.3753
71 5AAV GW5 2.38095
72 6FTB M0E 2.38095
73 2BJ4 OHT 2.38095
74 4TV1 36M 2.39044
75 3UUA 0CZ 2.39044
76 3UUD EST 2.39044
77 5B4B LP5 2.41935
78 2QE4 JJ3 2.41935
79 6AD9 KK4 2.43902
80 1M13 HYF 2.53165
81 5EY0 GTP 2.55474
82 4XF6 INS 2.5641
83 4XF6 ADP 2.5641
84 4XF6 LIP 2.5641
85 6DQU GLY ILE ILE ASN THR LEU 2.57009
86 2IZ1 RES 2.57009
87 2IZ1 ATR 2.57009
88 5OLK DTP 2.57009
89 4RZB NFQ 2.57009
90 1XON PIL 2.5788
91 2LBD REA 2.62172
92 3G58 988 2.62467
93 3GWN FAD 2.63158
94 6FX0 E9T 2.64317
95 2Z7I 742 2.64706
96 5DUF G7A 2.6616
97 2HW1 ANP 2.68456
98 1N46 PFA 2.71318
99 5HCY 60D 2.71903
100 3KFC 61X 2.7668
101 3HDY FAD 2.77078
102 3HDY FDA 2.77078
103 3HDY GDU 2.77078
104 5AEI LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 2.7972
105 6B2M COA 2.7972
106 1TV5 A26 2.80374
107 2GU8 796 2.80374
108 3G5N PB2 2.80374
109 3RS8 ALA TRP LEU PHE GLU ALA 2.80374
110 4DK7 0KS 2.83401
111 4BQS K2Q 2.84091
112 4BQS ADP 2.84091
113 2CB3 MLD 2.85714
114 4Q1A UDP 2.85714
115 4Q1A 2XZ 2.85714
116 4AZP A9M 2.89855
117 5N8V KZZ 2.89855
118 6GL8 F3Q 2.90698
119 5F1R 42O 2.95359
120 1FCZ 156 2.97872
121 5HZ5 65X 2.98507
122 4ORM FMN 2.99252
123 4ORM ORO 2.99252
124 4ORM 2V6 2.99252
125 2F5T MAL 3.00429
126 6A0S NDP 3.01205
127 5KAU RHQ 3.0303
128 2J1P GRG 3.03738
129 2IFB PLM 3.05344
130 5G57 6M5 3.05556
131 1YOK P6L 3.125
132 3L0E G58 3.16206
133 1WS1 BB2 3.20513
134 3GST GPR 3.22581
135 2PJL 047 3.23887
136 5VRH OLB 3.25671
137 1ZDU P3A 3.26531
138 2HFN FMN 3.26797
139 3GWT 066 3.27103
140 3T58 FAD 3.27103
141 6DIO CIT 3.27103
142 5NWI TYR PHE SER SEP ASN 3.27103
143 5CX6 CDP 3.27103
144 4WAS COO 3.2967
145 3RLF MAL 3.37838
146 5APK 76E 3.39623
147 4WPF 3SN 3.40909
148 3ATY FMN 3.43008
149 2AEL SAZ 3.47594
150 4U0S ADP 3.48837
151 3RYC GTP 3.4965
152 5LXT 7AK 3.4965
153 5LXT GDP 3.4965
154 2XN3 ID8 3.49854
155 5NTW 98N 3.50195
156 2A1L PCW 3.50467
157 6C1R EFD 3.50467
158 1XMY ROL 3.51759
159 1XMU ROF 3.51759
160 1XM4 PIL 3.51759
161 3V66 D3A 3.52941
162 3HST MLR 3.5461
163 4INW 1EY 3.57143
164 6F70 GSH 3.57143
165 1XVB 3BR 3.59897
166 5GUE GGS 3.62538
167 2HU5 GLY PHE 3.73832
168 5AG3 3EB 3.73832
169 6MVU K4V 3.73832
170 1U72 MTX 3.76344
171 1U72 NDP 3.76344
172 5NTP 98E 3.78151
173 3AI3 SOE 3.80228
174 4OGN 2U5 3.80952
175 5HCN DAO 3.83142
176 3GF4 FAD 3.84615
177 3GF4 U5P 3.84615
178 2ISJ FMN 3.91304
179 5OSW AE4 3.97196
180 2A3I C0R 3.97196
181 5MWY YNU 3.97196
182 5L7G 6QE 3.97196
183 5OSW DIU 3.97196
184 5HCV 60R 3.97196
185 1YWQ FMN 4
186 1YKD CMP 4.0201
187 2ZCQ B65 4.09556
188 1YYE 196 4.10448
189 1Z48 FMN 4.14201
190 4DXJ 0M9 4.14365
191 4OAS 2SW 4.16667
192 2W3L DRO 4.16667
193 4QVX 3CQ 4.19162
194 4POJ 2VP 4.20561
195 4COL DTP 4.20561
196 2OBD PCW 4.20561
197 1DKF BMS 4.20561
198 3FAL REA 4.20561
199 3FAL LO2 4.20561
200 5A4W QCT 4.24528
201 2WCJ M21 4.25532
202 2I0G I0G 4.28016
203 3LDW IPE 4.29293
204 3LDW ZOL 4.29293
205 4RW3 TDA 4.30464
206 3GKJ HC3 4.31034
207 3QKD HI0 4.41989
208 1UUO BRF 4.43925
209 1UUO FMN 4.43925
210 1UUO ORO 4.43925
211 4P6X HCY 4.43925
212 5LGD PLM 4.46927
213 5BVT PAM 4.47761
214 5Y24 GLY MET PRO ARG GLY ALA 4.54545
215 1U3R 338 4.56432
216 2YJD YJD 4.58333
217 4J26 EST 4.58333
218 3NJQ NJQ 4.66321
219 5Y02 HBX 4.6729
220 3FWN ATR 4.6729
221 3FWN 6PG 4.6729
222 2WPX ACO 4.71976
223 3FS1 MYR 4.78261
224 6D55 FWA 4.79042
225 3WH1 NAG NAG NAG NAG 4.85437
226 3SHZ 5CO 4.89914
227 1OPK MYR 4.90654
228 5DY5 5GR 4.93421
229 1YRX FMN 4.95868
230 2HZL PYR 5.14019
231 5UXM TRP 5.14019
232 3OKI OKI 5.15021
233 2BHW LUX 5.17241
234 4XU6 TDA 5.2381
235 1MT1 AG2 5.30973
236 1N13 AG2 5.30973
237 3CEV ARG 5.35117
238 2QQD AG2 5.35714
239 2QQC AG2 5.35714
240 5VZ0 2BA 5.37383
241 3ANP DCC 5.39216
242 3ANP DAO 5.39216
243 3QDC RET 5.43933
244 1XRO LEU 5.46075
245 2EW5 Y12 5.52486
246 2C0U FAD NBT 5.60748
247 2P1C GG3 5.64103
248 4HBM 0Y7 5.83333
249 1DQE BOM 5.83942
250 4NMC 2OP 5.84112
251 4NMC FAD 5.84112
252 2RHQ GAX 5.84112
253 3HP9 CF1 5.84112
254 5B0W 22B 5.84192
255 2F99 AKV 5.88235
256 6EWZ GTP 5.90717
257 4RHP PEF 5.95745
258 3KP6 SAL 5.96026
259 3KJD 78P 5.97826
260 3ZKI WZV 6.07477
261 1GNI OLA 6.07477
262 4OMJ 2TX 6.11511
263 4DR9 BB2 6.25
264 5CSD ACD 6.28931
265 2QCX PF1 6.46388
266 2R75 01G 6.50888
267 4LNU GTP 6.50888
268 1LN1 DLP 6.54206
269 4ETZ C2E 6.54206
270 4XB4 45D 6.57895
271 5V03 658 6.71141
272 3V49 PK0 6.76692
273 5BU2 ADP 6.7757
274 2CB8 MYA 6.89655
275 3RET SAL 6.93069
276 3RET PYR 6.93069
277 5TBM 79A 6.95652
278 2JC9 ADN 7.00935
279 2VG1 FPP 7.01754
280 3KYQ DPV 7.03518
281 3PMD 11A 7.18954
282 5SYN 71T 7.35931
283 4XVX P33 FDA 7.45501
284 3W54 RNB 7.47664
285 4F06 PHB 7.47664
286 2GBB CIT 7.69231
287 1MID LAP 7.69231
288 5L92 MLA 7.80488
289 5L92 C0R 7.80488
290 1HBK MYR 7.86517
291 3SE5 ANP 7.92683
292 3DCT 064 8.08511
293 5UC1 486 8.10811
294 1T0S BML 8.13953
295 1LQY BB2 8.15217
296 1QV1 CZH 8.20513
297 1JF0 CZH 8.20513
298 3RUU 37G 8.29694
299 5ICK FEZ 8.29694
300 2NU8 COA 8.41121
301 3A51 VDY 8.41121
302 1N20 3AG 8.64486
303 4RFM 3P6 8.64662
304 1D5Z ACE ALC ARG ALA ODA SER LEU NH2 8.83978
305 1OPB RET 8.95522
306 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 9
307 3FON VAL ASN ASP ILE PHE GLU ALA ILE 9
308 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 9
309 3QUZ QUV 9.09091
310 3SCM LGN 9.09091
311 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 9.09091
312 3RUG DB6 9.09091
313 3HUJ AGH 9.09091
314 1FO0 ILE ASN PHE ASP PHE ASN THR ILE 9.09091
315 5C9J DAO 9.09091
316 5LWY OLB 9.2437
317 2QM9 TDZ 9.67742
318 4FAJ LEU VAL THR LEU VAL PHE VAL 9.81308
319 5V3Y 5V8 10.8392
320 5MTE BB2 10.9489
321 1UVC STE 10.989
322 4FDV 0UK 11.0048
323 2FTB OLA 11.2
324 4BVM PLM 11.2782
325 4BVM VCA 11.2782
326 2HHP FLC 11.4486
327 5GPG RAP 11.828
328 3BEJ MUF 12
329 1FM9 9CR 12
330 1RDT L79 12
331 3IPQ 965 12
332 4HEE 14R 12
333 4DM8 REA 13.1086
334 1XAP TTB 13.1086
335 3RMK BML 13.253
336 5LGA 6VH 13.6667
337 2E2R 2OH 13.9344
338 2HFP NSI 14.2857
339 2RKN LP3 14.2857
340 3IIS PID 14.5695
341 3E3U NVC 14.7208
342 3IX9 MTX 15.7895
343 2F59 INI 16.5605
344 6A5Y 9CR 18.75
345 6A5Y 9R0 18.75
346 1I0S NAP 19.5266
347 4WN5 MVC 20
348 5G3N X28 20.4724
349 1PZL MYR 21.4286
350 4HIA FMN 22.7273
351 2DYS PSC 23.4043
352 5ZCO PSC 23.4043
353 5Z84 PSC 23.4043
354 2DYR PSC 23.4043
355 5ZCO PEK 23.4043
356 2DYR TGL 23.4043
357 5Z84 PEK 23.4043
358 5ZCO PGV 23.4043
359 5Z84 PGV 23.4043
360 2DYS TGL 23.4043
361 5Z84 TGL 23.4043
362 2DYR PEK 23.4043
363 5ZCO TGL 23.4043
364 2DYR PGV 23.4043
365 2DYS PEK 23.4043
366 4OGQ 7PH 24.1379
367 4OGQ 2WM 24.1379
368 4OGQ 3WM 24.1379
369 4J24 EST 31.5789
Pocket No.: 2; Query (leader) PDB : 1Q7E; Ligand: MET; 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: 1q7e.bio1) has 6 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1Q7E; Ligand: MET; Similar sites found with APoc: 38
This union binding pocket(no: 3) in the query (biounit: 1q7e.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 3AKI AH8 1.63551
2 3UG4 AHR 1.86916
3 6A46 DCM 1.95312
4 3ITA AIC 2.27273
5 1MJT ITU 2.30548
6 5L4R CPT 2.41546
7 1MVQ MMA 2.54237
8 5OVK NDP 2.73438
9 1RYD GLC 3.10078
10 4UYW H1S 3.13316
11 4CS9 AMP 3.1746
12 1UPR 4IP 3.25203
13 3R4S SLB 3.27103
14 3R75 PYR 3.73832
15 3AB4 LYS 3.93258
16 5A1S FLC 3.97196
17 3B6O TMP 4.04858
18 1YXM ADE 4.29043
19 2FKA BEF 4.65116
20 5YSI NCA 5.26316
21 1L7N ALF 5.6872
22 6GR0 F8W 5.74713
23 1P9B HDA 5.84112
24 1FQK ALF 5.84615
25 4BWL MN9 6.57895
26 5OCQ CIT 7.01754
27 4DS0 A2G GAL NAG FUC 7.97546
28 2WJH FLC 9.03614
29 5TCI MLI 10.1449
30 4F8L AES 11.4486
31 3HCH RSM 11.6438
32 1ZX5 LFR 12.3333
33 2QGI UDP 12.3832
34 1ZEI CRS 16.9811
35 2GCE RFC 27.5
36 2GCE SFC 27.5
37 1XA4 COA 39.486
38 1XVV CCQ 41.6667
Pocket No.: 4; Query (leader) PDB : 1Q7E; Ligand: MET; 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: 1q7e.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
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