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Receptor
PDB id Resolution Class Description Source Keywords
3L6C 2.2 Å EC: 5.1.1.18 X-RAY CRYSTAL STRUCTURE OF RAT SERINE RACEMASE IN COMPLEX WI MALONATE A POTENT INHIBITOR RATTUS NORVEGICUS PYRIDOXAL PHOSPHATE PLP SERINE RACEMASE ISOMERASE
Ref.: THE STRUCTURE OF MAMMALIAN SERINE RACEMASE: EVIDENC CONFORMATIONAL CHANGES UPON INHIBITOR BINDING. J.BIOL.CHEM. V. 285 12873 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MLI A:341;
B:341;
Valid;
Valid;
none;
none;
submit data
102.046 C3 H2 O4 C(C(=...
MN A:340;
B:340;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
PLP A:350;
B:350;
Part of Protein;
Part of Protein;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3L6C 2.2 Å EC: 5.1.1.18 X-RAY CRYSTAL STRUCTURE OF RAT SERINE RACEMASE IN COMPLEX WI MALONATE A POTENT INHIBITOR RATTUS NORVEGICUS PYRIDOXAL PHOSPHATE PLP SERINE RACEMASE ISOMERASE
Ref.: THE STRUCTURE OF MAMMALIAN SERINE RACEMASE: EVIDENC CONFORMATIONAL CHANGES UPON INHIBITOR BINDING. J.BIOL.CHEM. V. 285 12873 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3L6C - MLI C3 H2 O4 C(C(=O)[O-....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3L6B - MLI C3 H2 O4 C(C(=O)[O-....
2 3L6R - MLI C3 H2 O4 C(C(=O)[O-....
3 3L6C - MLI C3 H2 O4 C(C(=O)[O-....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2GN2 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
2 2ZR8 - SER C3 H7 N O3 C([C@@H](C....
3 1WTC - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
4 3L6B - MLI C3 H2 O4 C(C(=O)[O-....
5 3L6R - MLI C3 H2 O4 C(C(=O)[O-....
6 3L6C - MLI C3 H2 O4 C(C(=O)[O-....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MLI; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 MLI 1 1
2 OAA 0.5 0.666667
3 OXL 0.416667 0.642857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3L6C; Ligand: MLI; Similar sites found with APoc: 152
This union binding pocket(no: 1) in the query (biounit: 3l6c.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 3F6R FMN 0.589971
2 1U1W 3HA 1.00671
3 3U2U UDP 1.14068
4 2FCR FMN 1.15607
5 6B0K 9RN G4S 9RN G4S 1.17994
6 6B0K G4S 9RN G4S 9RN G4S 1.17994
7 4B2D FBP 1.76991
8 5XVS UDP 1.76991
9 4ZG4 VO4 ADP 1.76991
10 4KCT FDP 1.76991
11 5WS9 AMP 2.0649
12 2WOJ ADP ALF 2.0649
13 2VCH UDP 2.0649
14 1MDZ DCS 2.0649
15 1MDZ PLP 2.0649
16 1XG5 NAP 2.15054
17 3DAA PDD 2.52708
18 1LDN NAD 2.53165
19 1TLL FMN 2.65487
20 2FNU PMP UD1 2.65487
21 5Z69 AGS 2.65487
22 4K2M O1G 2.65487
23 2WPF WPF 2.94985
24 2WPF FAD 2.94985
25 2A2C NG1 2.94985
26 2A2C ADP 2.94985
27 2Q4W FAD 2.94985
28 3HQP FDP 2.94985
29 2GCO GNP 2.98507
30 2GCN GDP 2.98507
31 4YQE FMN 3.04569
32 4YQE PLQ 3.04569
33 2FLI DX5 3.18182
34 2C4J GSO 3.21101
35 3WGT FAD 3.24484
36 3WGT QSC 3.24484
37 5ZQY AR6 3.24484
38 1N1G BCP 3.24484
39 3RDO BTN 3.26797
40 4N82 FMN 3.37079
41 5XJ8 NKO 3.48259
42 5B3A 0JO 3.53982
43 2HJR APR 3.65854
44 4XOI GTP 3.7037
45 4BX7 B4F 3.7594
46 2CH5 NAG 3.83481
47 1NVM NAD 3.84615
48 2WC1 FMN 3.84615
49 5Z2M GTP 3.97727
50 2NVA PL2 4.03226
51 3W2E NAD 4.05904
52 3W2E FAD 4.05904
53 1AKV FMN 4.08163
54 4XSH GSP 4.10959
55 6BCB GSP 4.10959
56 3GST GPR 4.14747
57 5UMY TNN 4.28571
58 5WO4 B7V 4.30464
59 5NUL FMN 4.34783
60 2ALG HP6 4.34783
61 2ALG DAO 4.34783
62 4IP7 FBP 4.42478
63 1U7Z PMT 4.42478
64 1OW3 GDP 4.54545
65 6GAQ FMN 4.54545
66 2Q0L NAP 4.71976
67 4XVU ATP 4.78261
68 5G41 AP5 4.93274
69 1DUG GSH 5.12821
70 1VG9 GDP 5.30973
71 2OAT PFM 5.30973
72 1CZR FMN 5.32544
73 3MN6 ATP 5.34759
74 3MN9 ATP 5.34759
75 5VM0 9EG 5.46875
76 4B1W ATP 5.58511
77 1L3I SAH 5.8997
78 1MV8 NAD 5.8997
79 2J0V GDP 6.13208
80 4YKG FAD 6.19469
81 4YKG NAD 6.19469
82 1KXP ATP 6.19469
83 2Q97 ATP 6.19469
84 1RYH GNP 6.40394
85 6G1P CIT 6.48968
86 1N62 FAD 6.62651
87 3LXR GDP 6.77083
88 4DID GDP 6.78466
89 1A4R GDP 6.78466
90 1W8S FBP 6.84411
91 5HP8 PYR 7.25806
92 4ZAH T5K 7.37463
93 4HDH ATP 7.37463
94 5A8R TP7 7.37463
95 4R8L ASP 7.37463
96 2WPU KYT 7.54717
97 1Z08 GNP 7.64706
98 6EWR PMP 7.66962
99 1T57 FMN 7.76699
100 3P2E SAH 8
101 1T8U UAP SGN IDS SGN 8.25959
102 1T8U A3P 8.25959
103 5ECP ATP 8.55457
104 6BCA GSP 8.60927
105 2HV8 GTP 8.72093
106 5LJI FMN 8.78378
107 2JFN GLU 9.12281
108 1AG9 FMN 9.14286
109 4BMO FMN 9.2437
110 3QFA FAD 9.48276
111 1GSA ADP 9.49367
112 1O69 X04 10.1523
113 1NHX FTB 10.3245
114 1NHX PEP 10.3245
115 6FSG FMN 10.8844
116 1I7Q BEZ 10.9145
117 5XDR ADP 11.2094
118 5VL2 9EG 11.3636
119 4D9C PMP 11.5044
120 3KAP FMN 12.2449
121 4Z3X MTE 12.2905
122 4Z3X 4KX 12.2905
123 3GGF GVD 12.2924
124 5MZY 8EZ 13.3065
125 1LFD GNP 13.7931
126 2OM2 GDP 13.8889
127 5VEG FMN 14.0449
128 1I4D GDP 15.1042
129 4QYS PLP SEP 16.2242
130 5XKT GNP 18
131 1DS6 GDP 23.9583
132 1CX9 NHP 24.1888
133 6AMI TRP 24.4838
134 6AM8 PLT 24.7788
135 6CUZ FEV 24.7788
136 6AM8 TRP 24.7788
137 3VC3 C6P 27.1386
138 3PC3 P1T 27.7286
139 2PBD ATP 27.907
140 1VB3 KPA 28.0236
141 5I7A 68Q 28.8344
142 5D85 P1T 29.2035
143 4JBL MET 29.4985
144 4D9M 0JO 30.6785
145 3MN5 ATP 34.2105
146 3X44 PUS 35.8434
147 1V7C HEY 36.8732
148 6C2Z P1T 37.1681
149 1D6S PLP MET 38.5093
150 1D6S MET PLP 38.5093
151 3ZEI AWH 41.6129
152 2FF3 ATP 46.6667
Pocket No.: 2; Query (leader) PDB : 3L6C; Ligand: MLI; Similar sites found with APoc: 363
This union binding pocket(no: 2) in the query (biounit: 3l6c.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z2A GDP None
2 6AU6 GDP 0.884956
3 1G3M A3P 1.02041
4 1G3M PCQ 1.02041
5 3REF GDP 1.03093
6 2B4R NAD 1.15942
7 3QVV A3P 1.69492
8 3QVV 3QV 1.69492
9 2JL1 NAP 1.74216
10 1ZCB GDP 1.76991
11 5ZBC FAD 1.76991
12 1O3Y GTP 1.80723
13 2ZPT A3P 2.0339
14 3ZS9 ADP ALF 2.0649
15 1WPQ NAD 2.0649
16 4Y1B NAP 2.0649
17 1GR0 NAD 2.0649
18 3IO3 ADP 2.0649
19 5X2Z 3LM 2.0649
20 5Z21 NAI 2.0649
21 5JE8 NAD 2.0649
22 1GZ4 ATP 2.0649
23 1RPN NDP 2.08955
24 5NUF NAD 2.10843
25 5NUE NAD 2.10843
26 5KUT GDP 2.1164
27 1Y3A GDP 2.12766
28 2XTN GTP 2.13675
29 5X20 NAD 2.24359
30 1UPT GTP 2.33918
31 2OG2 MLI 2.35988
32 6DQU GLY ILE ILE ASN THR LEU 2.35988
33 3EYA FAD 2.35988
34 1YKJ FAD 2.35988
35 3ZXR IQ1 2.35988
36 3ZXR P3S 2.35988
37 3HU3 AGS 2.35988
38 1YBH FAD 2.35988
39 4ZKD GDP 2.35988
40 5X68 FAD 2.35988
41 4IDN GNP 2.35988
42 2AWN ADP 2.35988
43 1M7G ADP 2.36967
44 1M7G ADX 2.36967
45 1LC3 NAD 2.38095
46 1R4A GNP 2.42424
47 1F06 NDP 2.5
48 3PQC GDP 2.5641
49 2FJK 13P 2.62295
50 3B9Q MLI 2.64901
51 1RM0 NAI 2.65487
52 5M67 NAD 2.65487
53 5M67 ADE 2.65487
54 5M67 3D1 2.65487
55 1IHU ADP 2.65487
56 1TQ4 GDP 2.65487
57 1Z45 NAD 2.65487
58 3K5I AIR 2.65487
59 2CHG ANP 2.65487
60 5KSZ GCP 2.65487
61 1IHU AF3 2.65487
62 4PFO ADP 2.65487
63 4E5N NAD 2.72727
64 4B5W PYR 2.73438
65 2FAH GDP 2.94985
66 5EZ7 FAD 2.94985
67 1YTM ATP 2.94985
68 1QM5 GLC GLC GLC PO4 SGC GLC 2.94985
69 4EI7 GDP 2.94985
70 1GUZ NAD 2.94985
71 5NMX FAD 2.94985
72 1E3I CXF 2.94985
73 3UDG TMP 2.99003
74 4RZ3 ADP 3.05085
75 5K4W NAI 3.11526
76 5K4W THR 3.11526
77 3KO8 NAD 3.20513
78 3VX3 ADP 3.22581
79 4D3F NAP 3.22581
80 5HPY GDP 3.24324
81 2ZJ1 ARJ 3.24484
82 2ZJ1 NAD 3.24484
83 3NJ4 NAD 3.24484
84 3NJ4 AFX 3.24484
85 1KOR ARG 3.24484
86 1KOR SIN 3.24484
87 5UR0 NAD 3.24484
88 3WG6 NDP 3.25733
89 1KMQ GNP 3.26087
90 4Z0H NAD 3.29341
91 4V03 ADP 3.50195
92 1KEV NDP 3.53982
93 1GY8 NAD 3.53982
94 4AG5 ADP 3.53982
95 2VYN NAD 3.62538
96 1GAD NAD 3.63636
97 3TMK T5A 3.7037
98 1ION ADP 3.7037
99 1I1D 16G 3.72671
100 1I1D COA 3.72671
101 154L NAG NAG NAG 3.78378
102 1G3Q ADP 3.79747
103 2VVL FAD 3.83481
104 2VVM FAD 3.83481
105 1Z6T ADP 3.83481
106 3V1Y NAD 3.85757
107 5N2I NAP 3.87931
108 4NE2 SH2 3.89222
109 4NE2 ADP 3.89222
110 6BSX GDP 3.93258
111 2PV7 NAD 4.12979
112 4LYA ATP 4.12979
113 3WMX NAD 4.12979
114 4ZY1 4U5 4.12979
115 1F5N GNP 4.12979
116 3GGO NAI 4.14013
117 3GGO ENO 4.14013
118 1Z82 NDP 4.1791
119 1SQ5 ADP 4.22078
120 5Z75 NAD 4.28135
121 5ZZ6 NAD 4.32692
122 5ZZ6 ADP 4.32692
123 3LL5 IPE 4.41767
124 3LL5 ADP 4.41767
125 4CNK FAD 4.42478
126 4NZF ARB 4.42478
127 4B7X NAP 4.42478
128 4JBI NDP 4.42478
129 1JI0 ATP 4.42478
130 1H65 GDP 4.44444
131 5K5Z ANP 4.4586
132 3GJ3 GDP 4.52489
133 3GJ5 GDP 4.52489
134 3GJ8 GDP 4.52489
135 3M1I GTP 4.56621
136 6CI9 NAP 4.6332
137 2CUN 3PG 4.63415
138 3DOE GTP 4.6875
139 3B20 NAD 4.71976
140 3ABI NAD 4.71976
141 2I3G NAP 4.71976
142 6BKA FMN 4.71976
143 2GVC FAD 4.71976
144 2GV8 FAD 4.71976
145 2RGH FAD 4.71976
146 5A1T NAI 4.71976
147 5A1T OXM 4.71976
148 1VQW FAD 4.71976
149 5JCP GDP ALF 4.71976
150 5KSP GDP 4.73684
151 1RM4 NDP 4.74777
152 3FWY ADP 4.77707
153 4XTR ATP 4.78261
154 4XTR ADP 4.78261
155 1CER NAD 4.83384
156 2BME GNP 4.83871
157 5DIF GNP 4.8951
158 5UWP GNP 4.8951
159 5UWO GNP 4.8951
160 5UWH GNP 4.8951
161 5UWU GNP 4.8951
162 6CIT GNP 4.8951
163 5DHF GNP 4.8951
164 5UWW GNP 4.8951
165 5UWQ GNP 4.8951
166 5UWS GNP 4.8951
167 5UWR GNP 4.8951
168 3OND ADN 5.01475
169 3OND NAD 5.01475
170 4A0S NAP 5.01475
171 1RP0 AHZ 5.01475
172 3IHG FAD 5.01475
173 1QXO FMN 5.01475
174 1S8F GDP 5.08475
175 1L2T ATP 5.10638
176 2OFW ADX 5.28846
177 1JG3 ADN 5.30973
178 5GSN MMZ 5.30973
179 5GSN FAD 5.30973
180 1GQ2 NAP 5.30973
181 3BW2 FMN 5.30973
182 1ZEM NAD 5.34351
183 4PLT OXM 5.43807
184 4PLT NAI 5.43807
185 2V51 ATP 5.57029
186 5YEE ATP 5.57029
187 3WBF NAP 5.57377
188 3WBF API 5.57377
189 4B1V ATP 5.58511
190 1YAG ATP 5.6
191 4WZA ADP 5.60472
192 5J1J ANP 5.60472
193 4WZA ACP 5.60472
194 1FP6 ADP 5.60472
195 5AK0 8V1 5.60472
196 1W0J ADP BEF 5.60472
197 2GWH A3P 5.60472
198 5A96 GTP 5.62249
199 5Y8L HUI 5.76271
200 5Y8L NAD 5.76271
201 2YY7 NAD 5.76923
202 6FA4 GNP 5.78035
203 3N39 FMN 5.88235
204 2BEK ATP 5.8997
205 1PS9 FMN 5.8997
206 4K81 GTP 5.8997
207 1OFD FMN 5.8997
208 1IBR GNP 5.8997
209 5O9X G16 5.8997
210 2IXB NAD 5.8997
211 1OFD AKG 5.8997
212 4HAT GNP 5.8997
213 1MUU NAD 5.8997
214 3GJX GTP 5.8997
215 5T9F TYR 5.90406
216 5T9F NAP 5.90406
217 5O2T GSP 5.91716
218 1W7J ADP BEF 5.96026
219 5TB5 GDP 6
220 1CLU DBG 6.0241
221 3DDC GNP 6.0241
222 5N69 ADP 6.03015
223 3SFV GDP 6.07735
224 2PEZ DAT 6.14525
225 2PEZ GGZ 6.14525
226 5TOW NAI 6.19469
227 5TOW ADN 6.19469
228 5UPK GNP 6.19469
229 5ZZB ATP 6.19469
230 2FXU ATP 6.19469
231 2PAV ATP 6.19469
232 2A5F GTP 6.28571
233 3KB6 NAD 6.28743
234 3WYF GTP 6.30252
235 2BMZ XLM 6.38298
236 3FJO FMN 6.48968
237 3Q9L ATP 6.48968
238 3QJ4 FAD 6.48968
239 2FNA ADP 6.48968
240 3UIE ANP 6.5
241 5L3W GDP 6.53595
242 1KAO GDP 6.58683
243 2W83 GTP 6.66667
244 3CIF G3H 6.68524
245 3CIF NAD 6.68524
246 4ITR GDP 6.78466
247 1GRN GDP 6.78466
248 3DVA TPW 6.78466
249 1W85 TDP 6.78466
250 4YC7 GNP 6.78466
251 4ZOH MCN 6.78466
252 2NGR GDP 6.78466
253 1BVY FMN 6.78466
254 3PCR GTP 6.79012
255 5AYV NAP 6.79612
256 1GOT GDP 6.84932
257 6EBQ FMN 6.875
258 5WDR GNP 7.01754
259 1NF3 GNP 7.03125
260 2CVQ NDP 7.03364
261 2OZE AGS 7.04698
262 3GJ7 GDP 7.14286
263 1VL0 NAI 7.19178
264 1Z0K GTP 7.24638
265 4HEQ FMN 7.53425
266 1JAY NAP 7.54717
267 2R4J 13P 7.66962
268 2R4J FAD 7.66962
269 3A06 NDP 7.66962
270 2OHH FMN 7.66962
271 1OBV FMN 7.69231
272 5OJL TXP 7.71812
273 2FR1 NDP 7.81893
274 2WKQ GTP 7.83133
275 1OIV GDP 7.8534
276 1Z06 GNP 7.93651
277 5WPJ NDP 7.9646
278 3IID APR 8.05687
279 5Z20 NAI 8.11594
280 2IXE ATP 8.11808
281 1FQK GDP 8.16327
282 1EWY FAD 8.16327
283 3OJO NAD 8.25959
284 1UOZ GLC SSG SSG SGC 8.25959
285 5X0J AMP 8.26446
286 5X0J SEP 8.26446
287 1J5P NAD 8.3004
288 3ZQ6 ADP ALF 8.55457
289 1UMD TDP COI 8.55457
290 6BC0 GSP 8.66667
291 1HYH NAD 8.73786
292 2A92 NAI 9.03427
293 1R6B ADP 9.14454
294 3AB3 GDP 9.34959
295 4QM7 GTP 9.35672
296 3RFV 15L 9.3633
297 3RFV NAI 9.3633
298 5Y6Q FAD 9.39394
299 1V8B NAD 9.39457
300 4RQU NAD 9.43953
301 6B4K ANP 9.43953
302 6G14 G4P 9.52381
303 3CTL S6P 9.52381
304 6F3M NAD 9.73451
305 3FPZ AHZ 9.73451
306 5ZYN FAD 10.0295
307 5G5G FAD 10.0437
308 3E5H GNP 10.1124
309 2F5Z FAD 10.9375
310 1D2E GDP 11.2094
311 3X1Z GNP 11.3772
312 2JK0 ASP 11.6923
313 5BO9 CSF 11.7647
314 5BO9 SIA GAL NGS 11.7647
315 1X1R GDP 11.7978
316 1K6M AGS 12.6844
317 1X9I G6Q 12.9139
318 5UWT GNP 13.0435
319 5U5G NAP 13.2743
320 1GUA GNP 13.5802
321 5AOV NAP 13.6905
322 1E96 GTP 14.0625
323 3T1O GDP 14.4543
324 5EIN NAP 14.8148
325 4HDO GNP 15.3392
326 3SBD GNP 15.508
327 6D5M GNP 15.5689
328 6D5L GNP 15.5689
329 6D5J GNP 15.5689
330 6BVM GNP 15.5689
331 6D56 GNP 15.5689
332 6D5V GNP 15.5689
333 6BVK GNP 15.5689
334 6D59 GNP 15.5689
335 6D55 GNP 15.5689
336 6D5G GNP 15.5689
337 6BVJ GNP 15.5689
338 6BVL GNP 15.5689
339 6BVI GNP 15.5689
340 6D5E GNP 15.5689
341 6D5H GNP 15.5689
342 1MH1 GNP 15.5914
343 1NVV GNP 15.6627
344 3KUD GDP 15.6627
345 1WQ1 GDP 15.6627
346 1SOW NAD 15.9292
347 2FJU GSP 16.2921
348 1HE1 GDP 16.4773
349 1UAD GNP 16.5192
350 2A9K GDP 16.5192
351 1U8Z GDP 16.5192
352 3QV1 NAD 17.0732
353 2J59 GTP 17.8571
354 2GZ3 NAP 18.8791
355 4Q4K FMN 18.8791
356 1TU3 GNP 20.2532
357 3B1J NAD 24
358 1J2J GTP 24.4444
359 1ZC3 GNP 24.5714
360 5BXQ GDP 26.7717
361 3QF7 ANP 28
362 3ZIA ADP 31.1475
363 5UWI GNP 38.8889
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