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Receptor
PDB id Resolution Class Description Source Keywords
2VL1 2.15 Å EC: 3.5.1.6 CRYSTAL STRUCTURE OF BETA-ALANINE SYNTHASE FROM SACCHAROMYCE IN COMPLEX WITH A GLY-GLY PEPTIDE SACCHAROMYCES KLUYVERI HYDROLASE DI-ZINC CENTER AMIDOHYDROLASE ALPHA AND BETA PRCOMPLEX WITH GLYCINE-GLYCINE
Ref.: A RECRUITED PROTEASE IS INVOLVED IN CATABOLISM OF PYRIMIDINES. J.MOL.BIOL. V. 379 243 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLY GLY A:601;
B:601;
B:703;
C:601;
C:703;
C:805;
D:601;
D:703;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
Ki = 45 mM
132.119 n/a O=C([...
ZN A:500;
A:501;
B:500;
C:500;
D:500;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VL1 2.15 Å EC: 3.5.1.6 CRYSTAL STRUCTURE OF BETA-ALANINE SYNTHASE FROM SACCHAROMYCE IN COMPLEX WITH A GLY-GLY PEPTIDE SACCHAROMYCES KLUYVERI HYDROLASE DI-ZINC CENTER AMIDOHYDROLASE ALPHA AND BETA PRCOMPLEX WITH GLYCINE-GLYCINE
Ref.: A RECRUITED PROTEASE IS INVOLVED IN CATABOLISM OF PYRIMIDINES. J.MOL.BIOL. V. 379 243 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2V8G - BAL C3 H7 N O2 C(CN)C(=O)....
2 2VL1 Ki = 45 mM GLY GLY n/a n/a
3 2V8H - URP C4 H8 N2 O3 C(CNC(=O)N....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2V8G - BAL C3 H7 N O2 C(CN)C(=O)....
2 2VL1 Ki = 45 mM GLY GLY n/a n/a
3 2V8H - URP C4 H8 N2 O3 C(CNC(=O)N....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2V8G - BAL C3 H7 N O2 C(CN)C(=O)....
2 2VL1 Ki = 45 mM GLY GLY n/a n/a
3 2V8H - URP C4 H8 N2 O3 C(CNC(=O)N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLY GLY; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 GLY GLY 1 1
2 GLY GLY GLY 0.416667 0.935484
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VL1; Ligand: GLY GLY; Similar sites found with APoc: 30
This union binding pocket(no: 1) in the query (biounit: 2vl1.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4DYO SD4 1.68776
2 3AB1 FAD 1.94444
3 2Z48 NGA 2.08333
4 2ZOF BES 2.1097
5 6FX0 E9T 2.32068
6 2LBD REA 2.32068
7 1FCZ 156 2.55319
8 5K8P 6R8 2.58824
9 3LZW FAD 3.01205
10 1Z83 AP5 3.06122
11 1LFW AEP 3.82979
12 3EKK GS2 4.23453
13 3FED BIX 4.43038
14 6GAS FAD 4.53172
15 6GBX S77 4.55927
16 4X3R 686 5.48523
17 5VO3 SIN 5.52632
18 5XOY LYS 5.63003
19 3PB9 1BN 5.75758
20 1Y0Y L2O VAL VAL ASP 6.51558
21 1Q7L GLY 7.95455
22 3SI2 PBD 8.25688
23 1TXR BES 8.3612
24 3W6X HZP 8.73362
25 4F9U PBD 11.2179
26 1TF9 PHI 11.2676
27 1UKZ ADP 11.8227
28 4DM8 REA 40
29 4PXD 1AL 42.615
30 4PXE GLV 45.3488
Pocket No.: 2; Query (leader) PDB : 2VL1; Ligand: GLY GLY; 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: 2vl1.bio2) has 5 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2VL1; Ligand: GLY GLY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2vl1.bio2) has 5 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2VL1; Ligand: GLY GLY; Similar sites found with APoc: 5
This union binding pocket(no: 4) in the query (biounit: 2vl1.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3RUV ANP 1.68776
2 3MA0 XYP 3.51438
3 4BLW AMP 4.84429
4 5YB7 ORN 5.90717
5 5YB7 FAD 5.90717
Pocket No.: 5; Query (leader) PDB : 2VL1; Ligand: GLY GLY; Similar sites found with APoc: 412
This union binding pocket(no: 5) in the query (biounit: 2vl1.bio2) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 4ZH7 FUC GAL NAG GAL FUC 1.05485
3 1HV9 COA 1.31579
4 1O9J NAD 1.47679
5 3DLG GWE 1.47679
6 5L13 6ZE 1.47679
7 3C7A NAD 1.48515
8 4KBA 1QM 1.51057
9 5J75 6GQ 1.51515
10 5J5R IMP 1.54242
11 5J5R 6G1 1.54242
12 5KJW 53C 1.63934
13 5KD6 LBU 1.67064
14 5KD6 6C7 1.67064
15 1V25 ANP 1.68776
16 5X1M THG 1.68776
17 5X1M DHB 1.68776
18 2QE0 NAP 1.68776
19 5L2R MLA 1.68776
20 3UW5 MAA CHG PRO 0DQ 1.72414
21 3RHJ NAP 1.74081
22 4M73 M72 1.78042
23 4M73 SAH 1.78042
24 4DQ2 BTX 1.82927
25 5LRT ADP 1.89873
26 5A3T MMK 1.89873
27 1XL8 OCB 1.89873
28 5N5U 7N8 1.91083
29 4OYA 1VE 1.91489
30 1BW9 PPY 1.96629
31 1C1X HFA 1.97183
32 5EJL C2E 2.01613
33 4UTG ANP 2.02312
34 1QVJ RP5 2.05479
35 1UTJ ABN 2.06612
36 1X54 4AD 2.07373
37 2J3M ATP 2.1097
38 5KWW 6YA 2.1097
39 2GMH UQ5 2.1097
40 2J3M PRI 2.1097
41 4PZ2 NAD 2.1097
42 4J7H TLO 2.12314
43 4J7H TRH 2.12314
44 3SSO SAH 2.14797
45 2QIA U20 2.29008
46 2XCG XCG 2.32068
47 3IES M24 2.32068
48 4LGY ADP 2.32068
49 4L77 CNL 2.32068
50 4LY9 1YY 2.32068
51 4LY9 S6P 2.32068
52 5L2M 6ZY 2.32068
53 3TTC ADP 2.32068
54 3KRU FMN 2.33236
55 3ACL 3F1 2.36486
56 3VZ3 SSN 2.407
57 3VZ3 NAP 2.407
58 6BQ6 TER 2.41692
59 3OV6 MK0 2.51889
60 5AHN IMP 2.53165
61 3CW9 01A 2.53165
62 3HAZ NAD 2.53165
63 5MU6 MYA 2.55754
64 5MU6 KFK 2.55754
65 4NV7 COA 2.5641
66 3EFS BTN 2.57511
67 2Z3U CRR 2.58824
68 5XDT ZI7 2.5974
69 4RKX 3S9 2.68199
70 3NKS ACJ 2.74262
71 3X0D SAH 2.74262
72 3FYS PLM 2.74262
73 5X8G S0N 2.74262
74 2RG0 CTT 2.7907
75 6MPT C30 2.7972
76 1HXD BTN 2.80374
77 3WWX DIA 2.86533
78 1IXE COA 2.91777
79 3MVH WFE 2.92398
80 6D6L FY4 2.94118
81 4Z87 GDP 2.95359
82 5JFL NAD 2.95359
83 4Z87 5GP 2.95359
84 6GNO XDI 2.96296
85 5U3F 7TS 2.98913
86 2POC UD1 2.99728
87 4DXD 9PC 3.0303
88 3KYF 5GP 5GP 3.0303
89 4IGQ THR M3L GLN 3.05556
90 1S4M LUM 3.07167
91 3TUT ATP 3.07263
92 2RKV ZBA 3.10421
93 1V7C HEY 3.1339
94 4Z0G 5GP 3.1477
95 3TCT 3MI 3.14961
96 2YBP 2HG 3.14961
97 1VA6 P2S 3.16456
98 1VA6 ADP 3.16456
99 4C4A SAH 3.16456
100 4B0T ADP 3.16456
101 5DB3 58Q 3.16456
102 5TUF FAD 3.17848
103 6GW1 CHO 3.18471
104 4M37 SAH 3.207
105 1IYE PGU 3.23625
106 2BLE 5GP 3.26975
107 5F3I 5UJ 3.33333
108 12AS AMP 3.33333
109 4X9X OLA 3.34448
110 3FPF TNA 3.3557
111 5GP0 GPP 3.3557
112 3FPF MTA 3.3557
113 4WCX MET 3.37553
114 3TA2 AKG 3.38983
115 3H5N ATP 3.39943
116 2G30 ALA ALA PHE 3.48837
117 2I4O ATP 3.49345
118 5IOK ACE GLN THR ALA ARG KCR SER THR 3.52113
119 2Z5Y HRM 3.5865
120 5IVE 6E8 3.63636
121 6B3V ANP 3.68421
122 6B3V 7DQ 3.68421
123 3GZ8 APR 3.7037
124 1RE8 BD2 3.71429
125 3GC8 B45 3.78378
126 3RWP ABQ 3.79747
127 6E1Q CFA 3.79747
128 2ART LPA AMP 3.81679
129 2GU8 796 3.85757
130 5GS9 ARG 3.85757
131 4QMN DB8 3.87097
132 4IXH IMP 3.87812
133 2WSA 646 3.88128
134 2WSA MYA 3.88128
135 4NFN 2KC 3.8835
136 2V77 PAY 3.8835
137 2I7N ACO 3.88889
138 5FP4 YC8 3.89222
139 4NS3 NAD 3.90764
140 3OVR 5SP 3.94737
141 6HTO 5AD 4
142 6HTO MET 4
143 1OSS BEN 4.03587
144 1S3K FUC GAL NDG FUC 4.05405
145 3TWD GOB 4.05405
146 1PFK ADP 4.0625
147 3GRU AMP 4.0678
148 1CTU ZEB 4.08163
149 6GNC FAD 4.08163
150 3HXU A5A 4.08163
151 2Q8Z NUP 4.09357
152 2C5S AMP 4.11622
153 4AAW R84 4.13943
154 1SDW IYT 4.14013
155 1I7E IBS 4.15094
156 5O3Q CMP 4.16667
157 5ALC TIQ 4.16667
158 4IE6 UN9 4.21941
159 1NHX PEP 4.21941
160 1NHX FTB 4.21941
161 5OCG 9R5 4.2328
162 5M6N 7H9 4.23729
163 2AG4 LP3 4.26829
164 2AG4 OLA 4.26829
165 2C6Q NDP 4.2735
166 2C6Q IMP 4.2735
167 2ICK DMA 4.29185
168 5FLJ QUE 4.30108
169 4XP7 FNR 4.33526
170 4MTI 2DX 4.34783
171 5M06 ADP 4.34783
172 3QSB 743 4.37158
173 2P1M IHP 4.375
174 2P1O IHP 4.375
175 2P1O NLA 4.375
176 4CS4 ANP 4.37956
177 4CS4 AXZ 4.37956
178 5AE2 FYC 4.43038
179 5AE2 FAD 4.43038
180 5FWJ MMK 4.4586
181 2B9W FAD 4.48113
182 5Z2L NDP 4.4898
183 5WB6 9ZM 4.5082
184 5Q0F 9FA 4.5082
185 5VL2 9EG 4.54545
186 3BJK CIT 4.57516
187 4D42 W0I 4.60993
188 4D42 NAP 4.60993
189 1ZY5 ANP 4.62046
190 6FA4 D1W 4.62428
191 1Q0S SAH 4.6332
192 4RF7 ARG 4.64135
193 6DQU GLY ILE ILE ASN THR LEU 4.64135
194 6MVU K4V 4.64135
195 4NFE BEN 4.64135
196 4UWJ 7L5 4.6683
197 4UWJ MYA 4.6683
198 2YKL NLD 4.71698
199 2HRL SIA GAL SIA BGC NGA CEQ 4.72441
200 3F5O UOC COA 4.72973
201 2I8T GDD 4.79042
202 4HWT 1B2 4.84262
203 2YB9 HA0 4.85232
204 5N2D 8J8 4.86111
205 3E2M E2M 4.86486
206 6GVZ CHO 4.91803
207 3H2B SAH 4.92611
208 5B47 TPP 4.93421
209 5B47 PYR 4.93421
210 3NCQ ATP 5.04202
211 5MW4 5JU 5.08982
212 1JQD HSM 5.13699
213 1JQD SAH 5.13699
214 2AOT SAH 5.13699
215 2YC5 6BC 5.26316
216 3ZXR IQ1 5.27426
217 3ZXR P3S 5.27426
218 1LSH PLD 5.32915
219 4GN8 ASO 5.35117
220 6CZI 38E 5.35714
221 5LUN ARG 5.39773
222 5LUN OGA 5.39773
223 1B7Y FYA 5.48523
224 3BJU ATP 5.48523
225 4P5Z Q7M 5.54017
226 2WLG SOP 5.5814
227 2IU8 PLM 5.61497
228 3N6M GTP 5.62771
229 4K55 H6P 5.64516
230 3LVW GSH 5.6962
231 3VRY B43 5.72687
232 3NZ1 3NY 5.74713
233 1MGP PLM 5.7508
234 3A5Z KAA 5.75916
235 3A5Y KAA 5.7971
236 4C2C ALA VAL PRO ALA 5.8296
237 5TVA COA 5.83333
238 3C9U ADP 5.84795
239 2CC6 LUM 5.88235
240 4AF0 IMP 5.90717
241 1OPK P16 5.90717
242 1OFL NGK GCD 5.90717
243 1VPV PLM 6
244 2QK4 ATP 6.11814
245 4WUJ FMN 6.12245
246 3TKI S25 6.19195
247 5JIC ADP 6.22711
248 5JIC N7E 6.22711
249 4RD0 GDP 6.26506
250 4I7E PEP 6.26959
251 1Y7P RIP 6.27803
252 5E50 ALA TYR ASP GLU SEP TPO ASP GLU GLU 6.30631
253 1TRD PGH 6.4
254 3UW4 MAA CHG PRO 0DQ 6.52174
255 2Y6O 1N1 6.52921
256 4J4H 1J1 6.56371
257 4J4H NAI 6.56371
258 5DX8 SFG 6.59026
259 6ARJ SAH 6.59026
260 6ARJ BW4 6.59026
261 5DWQ SFG 6.59026
262 5DX0 SFG 6.59026
263 1ZM1 BGC BGC BGC 6.639
264 1N07 FMN 6.74847
265 4NS0 PIO 6.76692
266 2YNE YNE 6.77083
267 2YNE NHW 6.77083
268 4TXE 38F 6.80272
269 3PP0 03Q 6.80473
270 4CQE CQE 6.83453
271 1UYY BGC BGC 6.87023
272 3I3X U22 6.94981
273 2ZTG A5A 6.96203
274 4WO4 JLS 7
275 4XTX 590 7.03704
276 5WL1 CUY 7.07071
277 5WL1 D3D 7.07071
278 5U98 1KX 7.07071
279 5CPR 539 7.08955
280 6GW4 CHO 7.16612
281 1PVN MZP 7.18085
282 5T67 JHZ 7.21154
283 5FM0 WAQ 7.30769
284 2CM4 RCL 7.33333
285 1KDK DHT 7.34463
286 3IWD M2T 7.35294
287 5AEW BNL 7.44681
288 1XTP SAI 7.48031
289 3TAO PGH 7.49064
290 5BW4 SAM 7.49064
291 154L NAG NAG NAG 7.56757
292 2RCU BUJ 7.59494
293 2IVD ACJ 7.59494
294 4K3H 1OM 7.62712
295 1DZK PRZ 7.64331
296 4MOB ADP 7.83133
297 5UMY TNN 7.85714
298 2NXE SAM 7.87402
299 5DQ8 FLF 7.91667
300 1TT8 PHB 7.92683
301 1QDS PGA 7.96813
302 5YLT C7N 7.98479
303 5YLT SFG 7.98479
304 2GJ5 VD3 8.02469
305 1CCW TAR 8.0292
306 6B92 SAH 8.16327
307 5AHW CMP 8.16327
308 3PUN FUC GAL NDG FUC 8.22785
309 3K56 IS3 8.27068
310 5Y4R C2E 8.27586
311 5FUI APY 8.33333
312 1Y0G 8PP 8.37696
313 3G5D 1N1 8.39161
314 1NV8 SAM 8.4507
315 4Q0P 0MK 8.46154
316 4L3L 5FI 8.55263
317 5NIU 8YZ 8.59375
318 5VM0 9EG 8.59375
319 2Z1U ATP 8.74636
320 3LF0 ATP 8.77193
321 5AYT L6Y 8.80503
322 1DL5 SAH 8.83281
323 5OM2 DXT 8.94309
324 5XLY C2E 9.02256
325 4USI ATP 9.09091
326 5HZX 2GE 9.09091
327 2J9D ADP 9.2437
328 2J9C ATP 9.2437
329 3VBK COA 9.26829
330 3HKW IX6 9.2827
331 2DXU BT5 9.3617
332 2OJW ADP 9.375
333 6ALW BMJ 9.375
334 6ALW BNV 9.375
335 2AZ5 307 9.45946
336 5TZO 7V7 9.57447
337 5A89 FMN 9.61539
338 5A89 ADP 9.61539
339 2CJU PHX 9.73451
340 4J6W CTP 9.7561
341 4O9S 2RY 9.76744
342 3SJK LYS PRO VAL LEU ARG THR ALA 10
343 3LL5 IPE 10.0402
344 3LL5 ADP 10.0402
345 1T36 U 10.1266
346 2UX9 FMN 10.1449
347 3HUJ AGH 10.1626
348 3QXV MTX 10.3175
349 1A59 COA 10.3175
350 2RDE C2E 10.3586
351 3TAY MN0 10.4294
352 1I7M CG 10.4478
353 5JJU AMP 10.5882
354 3KPB SAM 10.6557
355 5L83 ASP TRP GLU ILE VAL 10.7143
356 5H2U 1N1 10.8614
357 2C49 ADN 10.9272
358 5OQW A4E 11.0236
359 1V3S ATP 11.2069
360 6EHH 2GE 11.3636
361 5DHU 5A8 11.3971
362 3KYG 5GP 5GP 11.4537
363 5DYO FLU 11.4679
364 2GJ3 FAD 11.6667
365 3H0L ADP 11.7021
366 1ERB ETR 12.0219
367 5N2F 8HW 12.0968
368 3ZLQ 6T9 12.1762
369 1H5R THM 12.2867
370 3CM2 X23 12.3077
371 1LNX URI 12.3457
372 5C83 4YN 12.7273
373 2XMY CDK 12.7517
374 3G08 FEE 13.1313
375 3RUG DB6 13.1313
376 5TVF CGQ 13.2308
377 4NG2 OHN 13.2743
378 2P5B OGA 13.6364
379 3DXY SAM 13.7615
380 5LXT GTP 13.986
381 4IEN GDP 14.1104
382 5ODY 9SK 14.4928
383 3E85 BSU 14.557
384 3LKJ LKJ 14.8936
385 1D9I 00P 14.9306
386 1SL3 170 14.9826
387 1W8S FBP 15.5894
388 1NFS DED 15.847
389 2YJ0 FMN 15.942
390 1PN4 HDC 16.0714
391 3AB4 LYS 16.2921
392 3DZ6 M8E 16.4179
393 2VSL MAA LYS PRO PHE 16.6667
394 4AX9 N5N 16.7315
395 1UWZ THU 16.9118
396 1WN3 HXC 16.9118
397 5HWV MBN 18.4615
398 4M38 SAH 19.0476
399 4R38 RBF 19.2857
400 5VWK PRO ALA TRP ASP GLU THR ASN LEU 19.6721
401 4RT1 C2E 20.5357
402 5EFW FMN 21.3793
403 1WPY BTN 21.7021
404 5U19 827 21.9941
405 5U19 SAH 21.9941
406 4F7E 0SH 22.449
407 3L9R L9R 22.449
408 3L9R L9Q 22.449
409 5UKL SIX 25.8065
410 6E2B PT7 26.3158
411 3MTX PGT 32.4503
412 1GJC 130 47.8261
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