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Receptor
PDB id Resolution Class Description Source Keywords
4L8F 1.97 Å EC: 3.4.19.9 CRYSTAL STRUCTURE OF GAMMA-GLUTAMYL HYDROLASE (C108A) COMPLE DANIO RERIO SANDWICHED-LIKE DOMAINS GAMMA-GLUTAMYL HYDROLASE HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE HYDROLYSIS AND POLYMOR METHOTREXATE POLYGLUTAMATE BY ZEBRAFISH GAMMA-GLUTA HYDROLASE J.MED.CHEM. V. 56 7625 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MTX D:301;
B:301;
Valid;
Valid;
none;
none;
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454.439 C20 H22 N8 O5 CN(Cc...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4L8F 1.97 Å EC: 3.4.19.9 CRYSTAL STRUCTURE OF GAMMA-GLUTAMYL HYDROLASE (C108A) COMPLE DANIO RERIO SANDWICHED-LIKE DOMAINS GAMMA-GLUTAMYL HYDROLASE HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE HYDROLYSIS AND POLYMOR METHOTREXATE POLYGLUTAMATE BY ZEBRAFISH GAMMA-GLUTA HYDROLASE J.MED.CHEM. V. 56 7625 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4L8F - MTX C20 H22 N8 O5 CN(Cc1cnc2....
2 4L8W - MTX DGL DGL n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4L8F - MTX C20 H22 N8 O5 CN(Cc1cnc2....
2 4L8W - MTX DGL DGL n/a n/a
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4L8F - MTX C20 H22 N8 O5 CN(Cc1cnc2....
2 4L8W - MTX DGL DGL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MTX; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 MTX 1 1
2 3BI 0.783505 0.884058
3 2MX 0.778947 0.924242
4 04J 0.663043 0.870968
5 MT1 0.632653 0.968254
6 MOT 0.534653 0.923077
7 COP 0.453782 0.815385
8 FOL 0.410714 0.779412
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4L8F; Ligand: MTX; Similar sites found with APoc: 355
This union binding pocket(no: 1) in the query (biounit: 4l8f.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 6C8X BVR None
2 2P3C 3TL None
3 3NWQ 2NC None
4 3GGU 017 None
5 3U7S 017 None
6 2P3B 3TL None
7 2J9D ADP None
8 3S43 478 None
9 3MWS 017 None
10 2FXD DR7 None
11 5T2Z 017 None
12 5IDM ANP 1.11732
13 2A92 NAI 1.28205
14 4GCZ ADP 1.2987
15 2Q7V FAD 1.60256
16 1A5Z NAD 1.60256
17 3KJS NAP 1.60256
18 5NN0 92H 1.60256
19 3KL3 GCU 1.60256
20 4P6G 2FZ 1.76991
21 5DUF G7A 1.90114
22 3UWV 2PG 1.91571
23 4D04 NAP 1.92308
24 4D04 FAD 1.92308
25 2VHW NAI 1.92308
26 4BV6 FAD 1.92308
27 5N0J FAD 1.92308
28 5K0A FAD 1.92308
29 3LZW FAD 1.92308
30 3LZW NAP 1.92308
31 6GAS FAD 1.92308
32 4M0R 644 1.92308
33 3WLE NAD 1.92308
34 5DDW 5B6 1.92308
35 1D4D FAD 1.92308
36 3FV3 IVA VAL VAL STA ALA STA 1.92308
37 3GFB NAD 1.92308
38 5VN0 FAD 1.92308
39 1CF2 NAP 1.92308
40 2O2C G6Q 1.92308
41 2CDU FAD 1.92308
42 1ZXM ANP 1.92308
43 3H7U NAP 1.92308
44 4NJS G08 2.0202
45 2AZC 3TL 2.0202
46 5LU5 M7P 2.03046
47 1JQD HSM 2.05479
48 1JQD SAH 2.05479
49 2DXU BT5 2.12766
50 3UOY NAP 2.24359
51 3UOY FAD 2.24359
52 2VVM FAD 2.24359
53 4TXI FAD 2.24359
54 5MZI FYK 2.24359
55 5MZI FAD 2.24359
56 1KOJ PAN 2.24359
57 5U8U FAD 2.24359
58 6GAR FAD 2.24359
59 2POC BG6 2.24359
60 1V59 FAD 2.24359
61 2BRY FAD 2.24359
62 1LVL FAD 2.24359
63 1V59 NAD 2.24359
64 1RYI FAD 2.24359
65 1LDN NAD 2.24359
66 4USR FAD 2.24359
67 2RGJ FAD 2.24359
68 3HQP FDP 2.24359
69 1MV8 NAD 2.24359
70 1RP0 AHZ 2.46479
71 5NMX NAP 2.5641
72 5NMX FAD 2.5641
73 3AXB FAD 2.5641
74 3AXB PRO 2.5641
75 2PZM NAD 2.5641
76 2PZM UDP 2.5641
77 1EGD FAD 2.5641
78 4RSL FAD 2.5641
79 4IXH IMP 2.5641
80 1X87 NAD 2.5641
81 1LTH NAD 2.5641
82 1GKZ ADP 2.5641
83 1FQ5 0GM 2.5641
84 5NII FAD 2.589
85 5JE8 NAD 2.64901
86 5OCM NAP 2.74914
87 6F3N NAD 2.88462
88 6F3N ADN 2.88462
89 6F3M NAD 2.88462
90 1V8B NAD 2.88462
91 4CZG ADP 2.88462
92 3HDY GDU 2.88462
93 2C6Q NDP 2.88462
94 3HDY FAD 2.88462
95 4REP FAD 2.88462
96 2C6Q IMP 2.88462
97 3X0V FAD 2.88462
98 4IV9 FAD 2.88462
99 2DKH FAD 2.88462
100 2DKH 3HB 2.88462
101 5X8G S0N 2.88462
102 2UUU FAD 2.88462
103 3OJO NAD 2.88462
104 5ZZ6 NAD 2.88462
105 5ZZ6 ADP 2.88462
106 4IZC 1GZ 2.90909
107 5OJL TXP 3.02013
108 3T3C 017 3.0303
109 4J4H 1J1 3.0888
110 4J4H NAI 3.0888
111 4JK3 NAD 3.0888
112 3G6N MET ALA SER 3.14136
113 4YKG NAD 3.20513
114 5BJX UDP 3.20513
115 5BJX NAD 3.20513
116 3OND NAD 3.20513
117 3OND ADN 3.20513
118 3LAD FAD 3.20513
119 4D9M 0JO 3.20513
120 4JNE ATP 3.20513
121 5UR0 NAD 3.20513
122 2DFV NAD 3.20513
123 5ZEC NAP 3.20513
124 3MQ2 SAH 3.21101
125 3VPH NAD 3.22581
126 1ZEM NAD 3.43511
127 2XOC ADP 3.44828
128 1REO FAD 3.52564
129 3NJ4 AFX 3.52564
130 3NJ4 NAD 3.52564
131 4C2G ALA ALA ALA ALA 3.52564
132 5WGR FAD 3.52564
133 2QZX IVA VAL VAL STA ALA STA 3.52564
134 1JQI FAD 3.52564
135 4MDH NAD 3.52564
136 4Z24 FAD 3.52564
137 1Y8Q ATP 3.52564
138 1SC6 NAD 3.52564
139 3MAG SAH 3.58306
140 3MCT SAH 3.7037
141 4YCA NDP 3.7415
142 2DT5 NAD 3.79147
143 4RHE FMN 3.82775
144 2GVC FAD 3.84615
145 5G3U ITW 3.84615
146 2GV8 FAD 3.84615
147 2ZJ1 ARJ 3.84615
148 2ZJ1 NAD 3.84615
149 5NUF NAD 3.84615
150 1VQW FAD 3.84615
151 5BUK FAD 3.84615
152 5BVA FAD 3.84615
153 5TDF 7A3 3.84615
154 5NUE NAD 3.84615
155 5TE1 7A2 3.84615
156 2ZKJ ADP 3.84615
157 2PT9 2MH 3.84615
158 2CXS F6P 3.84615
159 5G3U FDA 3.84615
160 1CDO NAD 3.84615
161 2PT9 S4M 3.84615
162 1TLL FMN 3.84615
163 3FSM 2NC 3.94089
164 3KA2 2NC 3.94089
165 6A4R ASP 4.15094
166 2CVZ NDP 4.15225
167 2IVD FAD 4.16667
168 1UWK URO 4.16667
169 1UWK NAD 4.16667
170 2Q1W NAD 4.16667
171 5TOW NAI 4.16667
172 5TOW ADN 4.16667
173 4NTC FAD 4.16667
174 2VVL FAD 4.16667
175 1SAY PYR 4.16667
176 2I7C AAT 4.24028
177 1XCL SAH 4.25532
178 1JXZ BCA 4.46097
179 3B1F NAD 4.48276
180 2IID PHE 4.48718
181 2IID FAD 4.48718
182 2XVF FAD 4.48718
183 4JNA FAD 4.48718
184 1DJN ADP 4.48718
185 1Q1R FAD 4.48718
186 6BQ6 TER 4.48718
187 5XHA FRU 4.48718
188 5Z21 NAI 4.48718
189 1WP4 NDP 4.49827
190 3UWB BB2 4.54545
191 2DTX BMA 4.54545
192 2F1K NAP 4.6595
193 1L3I SAH 4.6875
194 2YG3 FAD 4.80769
195 5M67 3D1 4.80769
196 5M67 NAD 4.80769
197 5M67 ADE 4.80769
198 2YVF FAD 4.80769
199 2YVF NAD 4.80769
200 3GD4 FAD 4.80769
201 2YVJ NAI 4.80769
202 3GD4 NAD 4.80769
203 3AYI FAD 4.80769
204 3AYI HCI 4.80769
205 4NW6 2NS 4.80769
206 3E1T FAD 4.80769
207 5I39 FAD 4.80769
208 2YYY NAP 4.80769
209 1LLF F23 4.80769
210 3EMY IVA VAL VAL STA ALA STA 4.80769
211 5JFL NAD 4.80769
212 2XYQ SAH 4.91803
213 5O3Q CMP 5
214 1P1C SAH 5.02513
215 4YHQ G10 5.05051
216 4M8X KGQ 5.05051
217 3WGT QSC 5.12821
218 3WGT FAD 5.12821
219 1J49 NAD 5.12821
220 5MBX SP5 5.12821
221 5MBX FAD 5.12821
222 6F97 FAD 5.12821
223 5E4R NAP 5.12821
224 4RVG TYD 5.12821
225 5FJN FAD 5.12821
226 5FJN BE2 5.12821
227 3QFU ADP 5.12821
228 5N6C NAD 5.33333
229 3WDM ADN 5.36398
230 5X68 FAD 5.44872
231 4E5N NAD 5.44872
232 5J60 FAD 5.44872
233 2QA1 FAD 5.44872
234 3BNK FMN 5.61225
235 5TS5 FAD 5.76923
236 1H82 FAD 5.76923
237 1H82 GZZ 5.76923
238 3K7M FAD 5.76923
239 3L9W AMP 5.76923
240 5TWB FAD 5.76923
241 4DSG UDP 5.76923
242 4DSG FAD 5.76923
243 3Q9T FAY 5.76923
244 3L9W GSH 5.76923
245 4ZSI GLP 5.84795
246 2NV2 GLN 5.88235
247 1G27 BB1 5.95238
248 4YDX TCE 5.97015
249 1MO9 KPC 6.08974
250 1MO9 FAD 6.08974
251 2HQM FAD 6.08974
252 1YY5 FAD 6.08974
253 4JDR FAD 6.08974
254 3NYC IAR 6.08974
255 3NYC FAD 6.08974
256 1ZGD NAP 6.08974
257 2ZL4 ALA ALA ALA ALA 6.12245
258 1U7Z PMT 6.19469
259 1KEV NDP 6.41026
260 4CNK FAD 6.41026
261 2Y6Q FAD 6.41026
262 2Y6Q I7T 6.41026
263 1I8T FAD 6.41026
264 1GZ6 NAI 6.41026
265 5TTJ FAD 6.53061
266 3NCQ ATP 6.72269
267 4AP3 FAD 6.73077
268 4AP3 NAP 6.73077
269 2RAB NAD 6.73077
270 2RAB FAD 6.73077
271 5J5Z FAD 6.73077
272 2B9W FAD 6.73077
273 3RNM FAD 6.73077
274 4KP7 NAP 6.73077
275 4KP7 1UQ 6.73077
276 2F5Z FAD 6.73077
277 4II2 ATP 6.73077
278 4Q5M ROC 6.89655
279 2ZJ3 G6P 6.93333
280 2WOE AR6 7.02341
281 2OKL BB2 7.02703
282 5MIT FAD 7.05128
283 5MIT NAP 7.05128
284 5HSA FAS 7.05128
285 1RSG FAD 7.05128
286 3FPZ AHZ 7.05128
287 1QO8 FAD 7.05128
288 4USQ FAD 7.05128
289 3AD8 NAD 7.07071
290 2O07 MTA 7.23684
291 2O07 SPD 7.23684
292 3M6P BB2 7.25389
293 5GSN MMZ 7.37179
294 5GSN FAD 7.37179
295 5GSN NAP 7.37179
296 4FWE FAD 7.37179
297 4XFR CIT 7.37179
298 3AB1 FAD 7.37179
299 4K5S FAD 7.37179
300 3JYN NDP 7.37179
301 5JCA FAD 7.39437
302 3RFV 15L 7.49064
303 3RFV NAI 7.49064
304 2GAG NAD 7.61905
305 1VCO GLN 7.69231
306 1GET FAD 7.69231
307 1GET NAP 7.69231
308 4ZCC NAI 7.69231
309 4ZCC FAD 7.69231
310 5KMS NAD 7.69231
311 3QJ4 FAD 7.69231
312 1XXA ARG 7.69231
313 4QIJ 1HA 7.69231
314 4YSX FAD 7.97872
315 3KLJ FAD 8.01282
316 1MOQ GLP 8.01282
317 4AMV F6R 8.01282
318 1HYE NAP 8.01282
319 1O94 ADP 8.33333
320 5EZ7 FAD 8.65385
321 2E5V FAD 8.65385
322 6ASZ GLN THR ALA ARG M3L SER 8.69565
323 1TYU GLA MAN RAM TYV GLA MAN RAM TYV 8.97436
324 3LU1 NAD 8.97436
325 2IXB NAD 8.97436
326 1RL4 BRR 9.04255
327 2Z3Y F2N 9.29487
328 3D36 ADP 9.83607
329 4ZY1 4U5 9.9359
330 2NP9 YE1 9.9359
331 1SIV PSI 10.101
332 5CXX FER 10.1818
333 4NTD FAD 10.2564
334 2F6U CIT 10.2564
335 5KY5 GDP 10.2564
336 5UXH GFB 10.2564
337 5KY9 GDP 10.2564
338 5KXQ GDP 10.2564
339 3ICT FAD 11.2179
340 3ICR FAD 11.2179
341 5ODQ FAD 11.4286
342 6FIV 3TL 11.5044
343 6FHO FAD 12.5
344 4MO2 FDA 12.5
345 4MO2 FAD 12.5
346 4NMC 2OP 12.5
347 4NMC FAD 12.5
348 4HSU FAD 15.3226
349 1HYH NAD 16.1812
350 1H8P PC 16.5138
351 1GPM CIT 17.6282
352 1S17 GNR 17.7778
353 1IDA 0PO 19.1919
354 2D37 FMN 19.8864
355 2D37 NAD 19.8864
Pocket No.: 2; Query (leader) PDB : 4L8F; Ligand: MTX; Similar sites found with APoc: 64
This union binding pocket(no: 2) in the query (biounit: 4l8f.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 6AA8 NAD 0.993378
2 1YKJ FAD 1.92308
3 9LDB NAD 1.92308
4 9LDT NAD 1.92308
5 4JJF FE9 1.92308
6 4JJF N2I 1.92308
7 1RYI GOA 2.24359
8 1XFF GLU 2.5
9 1UDY FAD 2.5641
10 4YNU FAD 2.5641
11 1GTE IUR 2.5641
12 1GTE FMN 2.5641
13 4PIV NDP 2.5641
14 1DSS NAD 2.5641
15 4WOP CTP 2.66667
16 4NAE 1GP 2.66667
17 5Y8L NAD 3.05085
18 5Y8L HUI 3.05085
19 5AHM IMP 3.20513
20 5YB7 FAD 3.20513
21 5YB7 ORN 3.20513
22 5WA0 MSS 3.20513
23 1FL2 FAD 3.22581
24 3VPH OXM 3.22581
25 4G9E C4L 3.22581
26 1ZBQ NAD 3.52564
27 6ER9 NAP 3.84615
28 6ER9 FAD 3.84615
29 1MUU NAD 3.84615
30 1C1X NAD 3.84615
31 5ZYN FAD 3.84615
32 1BW9 NAD 3.84615
33 1V25 ANP 4.16667
34 1HKU NAD 4.16667
35 4Z0H NAD 4.16667
36 5U5G NAP 4.40678
37 4UP4 NDG 4.48718
38 2XVE FAD 4.80769
39 4X9M FAD 4.80769
40 1WS1 BB2 5.12821
41 1D1T NAD 5.12821
42 3MQG ACO 5.20833
43 3QUR FM4 5.59441
44 3QUR ADP 5.59441
45 5G1X ADP 5.96491
46 1J0X NAD 6.08974
47 6ASY ATP 6.41026
48 1YKF NAP 6.41026
49 4D7E FAD 6.41026
50 4L8V NAP 6.41026
51 3FJO FMN 7.05128
52 3UCL FAD 7.37179
53 3UCL CYH 7.37179
54 3UCL NAP 7.37179
55 4K5S PM0 7.37179
56 1EQ2 NAP 7.41935
57 2G5C NAD 7.47331
58 5A0R ACE GLU VAL ASN PRO 8.08081
59 3F8D FAD 8.97436
60 2A14 SAH 9.12547
61 3A4V NAD 10.5769
62 3ICS FAD 11.2179
63 2FZW NAD 12.0643
64 4GUS FAD 15.3226
Pocket No.: 3; Query (leader) PDB : 4L8F; Ligand: MTX; 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: 4l8f.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4L8F; Ligand: MTX; 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: 4l8f.bio3) has 12 residues
No: Leader PDB Ligand Sequence Similarity
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