Receptor
PDB id Resolution Class Description Source Keywords
4IYO 1.8 Å EC: 4.4.1.1 CRYSTAL STRUCTURE OF CYSTATHIONINE GAMMA LYASE FROM XANTHOMO PV. ORYZAE (XOMETC) IN COMPLEX WITH E-SITE SERINE, A-SITE SS ITE EXTERNAL ALDIMINE STRUCTURE WITH AMINOACRYLATE AND A-SIM INOPROPIONATE INTERMEDIATES XANTHOMONAS ORYZAE PV. ORYZAE PLP DEPENDENT ENZYME LYASE XOCGL IMINOPROPIONATE SERINEMETABOLISM PLP DEPENDENT ENZYME CYSTATHIONINE GAMMA LYASEBINDING
Ref.: PLP UNDERGOES CONFORMATIONAL CHANGES DURING THE COU ENZYMATIC REACTION. ACTA CRYSTALLOGR.,SECT.D V. 70 596 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL D:403;
A:402;
C:403;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
0JO A:404;
 Valid;
 none;
 submit data
316.204 C11 H13 N2 O7 P Cc1c(...
NAK B:402;
C:402;
 Valid;
Valid;
 none;
none;
 submit data
87.077 C3 H5 N O2 CC(=[...
PYR B:403;
 Invalid;
 none;
 submit data
88.062 C3 H4 O3 CC(=O...
SO4 A:403;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4IYO 1.8 Å EC: 4.4.1.1 CRYSTAL STRUCTURE OF CYSTATHIONINE GAMMA LYASE FROM XANTHOMO PV. ORYZAE (XOMETC) IN COMPLEX WITH E-SITE SERINE, A-SITE SS ITE EXTERNAL ALDIMINE STRUCTURE WITH AMINOACRYLATE AND A-SIM INOPROPIONATE INTERMEDIATES XANTHOMONAS ORYZAE PV. ORYZAE PLP DEPENDENT ENZYME LYASE XOCGL IMINOPROPIONATE SERINEMETABOLISM PLP DEPENDENT ENZYME CYSTATHIONINE GAMMA LYASEBINDING
Ref.: PLP UNDERGOES CONFORMATIONAL CHANGES DURING THE COU ENZYMATIC REACTION. ACTA CRYSTALLOGR.,SECT.D V. 70 596 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4IYO - 0JO C11 H13 N2 O7 P Cc1c(c(c(c....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4IYO - 0JO C11 H13 N2 O7 P Cc1c(c(c(c....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4IYO - 0JO C11 H13 N2 O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 0JO; Similar ligands found: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 0JO 1 1
2 4LM 0.71875 0.946429
3 FEV 0.69697 0.929825
4 F0G 0.656716 0.892857
5 KOU 0.647059 0.864407
6 EVM 0.637681 0.85
7 Z98 0.625 0.809524
8 EXT 0.61194 0.830508
9 PL6 0.611111 0.87931
10 FEJ 0.60274 0.847458
11 EPC 0.597015 0.857143
12 PZP 0.590164 0.807018
13 FOO 0.588235 0.877193
14 PLP 0.57377 0.803571
15 AN7 0.573529 0.839286
16 P3D 0.569444 0.738462
17 P70 0.564103 0.894737
18 PL5 0.564103 0.836066
19 PUS 0.564103 0.73913
20 MPM 0.56338 0.844828
21 5DK 0.5625 0.784615
22 EQJ 0.5625 0.784615
23 HCP 0.547945 0.803279
24 GLY PLP 0.541667 0.779661
25 P89 0.530864 0.720588
26 6DF 0.526316 0.810345
27 PLP ABU 0.519481 0.770492
28 Q0P 0.511628 0.822581
29 PLT 0.5 0.822581
30 PFM 0.5 0.864407
31 PLP 999 0.5 0.79661
32 SER PLP 0.493506 0.813559
33 PLP PUT 0.493506 0.707692
34 PLP ALO 0.487179 0.79661
35 LUH 0.470588 0.694444
36 LUK 0.470588 0.694444
37 O1G 0.465116 0.753846
38 PMP 0.462687 0.714286
39 P1T 0.460526 0.828125
40 PLR 0.453125 0.754386
41 PLP PHE 0.448276 0.79661
42 C6P 0.443038 0.753846
43 PDD 0.441558 0.738462
44 PDA 0.441558 0.738462
45 PP3 0.441558 0.738462
46 CKT 0.435897 0.822581
47 TLP 0.43038 0.738462
48 2BK 0.43038 0.738462
49 2BO 0.43038 0.738462
50 PLS 0.43038 0.753846
51 PLP PVH 0.428571 0.720588
52 9TD 0.427083 0.728571
53 PXP 0.426471 0.704918
54 PPD 0.425 0.753846
55 L7N 0.421687 0.657895
56 PLG 0.421053 0.727273
57 P0P 0.42029 0.77193
58 PY5 0.419753 0.710145
59 PY6 0.416667 0.690141
60 GT1 0.414286 0.68254
61 PLP 142 0.410526 0.720588
62 7XF 0.409639 0.731343
63 PGU 0.409639 0.731343
64 PDG 0.409639 0.731343
65 ILP 0.409639 0.716418
66 PPG 0.409091 0.8
67 LPI 0.404762 0.680556
68 QLP 0.404762 0.690141
69 IN5 0.402597 0.707692
70 HEY 0.4 0.761194
71 IK2 0.4 0.720588
Ligand no: 2; Ligand: NAK; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 NAK 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 0JO; Similar ligands found: 47
No: Ligand Similarity coefficient
1 PLI 0.9787
2 PLP SER 0.9777
3 5PA 0.9668
4 PLP GLY 0.9616
5 DCS 0.9603
6 LCS 0.9543
7 OJQ 0.9449
8 PLP AOA 0.9442
9 PMH 0.9353
10 7TS 0.9324
11 PLP CYS 0.9318
12 PM9 0.9110
13 PLP 2TL 0.9082
14 PLP MET 0.9038
15 MET PLP 0.9008
16 3LM 0.8976
17 07U 0.8931
18 PSZ 0.8924
19 74U 0.8875
20 HM5 0.8865
21 PLP 2KZ 0.8856
22 KET 0.8855
23 UI2 0.8829
24 ASP PLP 0.8762
25 P57 0.8744
26 IRG 0.8726
27 2T4 0.8712
28 855 0.8692
29 4FY 0.8667
30 PLP 2ML 0.8663
31 5F3 0.8661
32 LEU PLP 0.8652
33 KS1 0.8643
34 G16 0.8634
35 KB8 0.8632
36 3QP 0.8596
37 BPG 0.8590
38 ROL 0.8573
39 580 0.8570
40 7CU 0.8560
41 VKE 0.8554
42 33P 0.8545
43 NCN 0.8543
44 8HH 0.8528
45 PLA 0.8519
46 SER A2G 0.8518
47 PLP 0A0 0.8515
Ligand no: 2; Ligand: NAK; Similar ligands found: 302
No: Ligand Similarity coefficient
1 OXM 1.0000
2 HBS 1.0000
3 ALA 1.0000
4 2OP 1.0000
5 HGY 1.0000
6 OXD 1.0000
7 LAC 1.0000
8 BUO 1.0000
9 PYM 1.0000
10 OXL 1.0000
11 PYR 1.0000
12 HBR 0.9997
13 DAL 0.9981
14 5Y9 0.9964
15 ALQ 0.9963
16 NIS 0.9912
17 1AC 0.9765
18 TF4 0.9723
19 FAH 0.9705
20 PPI 0.9662
21 AOA 0.9652
22 GLY 0.9647
23 NIE 0.9645
24 DXX 0.9644
25 GOA 0.9644
26 GLV 0.9637
27 3TR 0.9611
28 SER 0.9601
29 HUI 0.9601
30 MB3 0.9591
31 SAR 0.9588
32 2KT 0.9584
33 BAL 0.9581
34 BMD 0.9578
35 DE2 0.9574
36 BUA 0.9573
37 39J 0.9568
38 DBB 0.9566
39 HIU 0.9564
40 KG7 0.9558
41 SMB 0.9555
42 A3B 0.9536
43 CYS 0.9532
44 AKR 0.9528
45 03W 0.9526
46 F3V 0.9519
47 TAY 0.9519
48 3PY 0.9507
49 BAQ 0.9506
50 DSN 0.9503
51 R3W 0.9503
52 HSL 0.9501
53 ALF 0.9496
54 4MZ 0.9488
55 DMI 0.9465
56 BU4 0.9460
57 HAE 0.9459
58 0PY 0.9457
59 5KX 0.9447
60 ATO 0.9446
61 ABA 0.9443
62 2MZ 0.9443
63 F50 0.9439
64 3OH 0.9437
65 2RA 0.9434
66 MLI 0.9432
67 XAP 0.9431
68 P1R 0.9427
69 BNZ 0.9421
70 MMZ 0.9419
71 1CB 0.9416
72 3ZS 0.9413
73 GBL 0.9410
74 HVB 0.9410
75 MEU 0.9408
76 B20 0.9407
77 3BB 0.9402
78 2A3 0.9400
79 3MT 0.9395
80 JZ6 0.9393
81 2AI 0.9374
82 4AX 0.9371
83 NHY 0.9370
84 GOL 0.9370
85 HLT 0.9369
86 PXO 0.9358
87 C2N 0.9355
88 HOW 0.9355
89 PPF 0.9353
90 KSW 0.9351
91 NMU 0.9350
92 PHZ 0.9348
93 BUB 0.9343
94 DTI 0.9336
95 2A1 0.9334
96 MTG 0.9332
97 1MZ 0.9328
98 BYZ 0.9326
99 AGU 0.9324
100 DCY 0.9323
101 MR3 0.9322
102 DGY 0.9318
103 MGX 0.9311
104 BXA 0.9304
105 ATQ 0.9298
106 BRP 0.9283
107 6SP 0.9277
108 61G 0.9273
109 TRI 0.9267
110 AMT 0.9266
111 7EX 0.9265
112 MLA 0.9264
113 BUQ 0.9255
114 5MP 0.9254
115 HV2 0.9248
116 TSZ 0.9235
117 2HA 0.9231
118 IMD 0.9230
119 C5J 0.9223
120 PZO 0.9220
121 GXV 0.9214
122 IPH 0.9212
123 J3K 0.9211
124 ETF 0.9209
125 EGD 0.9205
126 HUH 0.9201
127 L60 0.9198
128 3HR 0.9194
129 9PO 0.9192
130 2IM 0.9190
131 24T 0.9190
132 192 0.9188
133 DMG 0.9181
134 PYZ 0.9179
135 ES3 0.9177
136 MLM 0.9170
137 HYN 0.9170
138 93B 0.9169
139 3HL 0.9169
140 A2Q 0.9165
141 3GR 0.9159
142 XIX 0.9158
143 CEJ 0.9158
144 LER 0.9156
145 DTL 0.9155
146 MZY 0.9140
147 23W 0.9133
148 2AP 0.9132
149 HVK 0.9132
150 LGA 0.9122
151 1BP 0.9122
152 L89 0.9121
153 IVA 0.9121
154 3AP 0.9119
155 3CL 0.9118
156 MZ0 0.9109
157 MBN 0.9107
158 HRZ 0.9106
159 93Q 0.9104
160 CAQ 0.9101
161 4AP 0.9099
162 9A4 0.9098
163 BXO 0.9097
164 CHT 0.9096
165 NVI 0.9095
166 938 0.9092
167 THR 0.9089
168 76X 0.9082
169 CYH 0.9080
170 CXL 0.9080
171 FP2 0.9077
172 BEW 0.9072
173 MRY 0.9071
174 HAI 0.9070
175 WOT 0.9070
176 1AN 0.9070
177 2AF 0.9066
178 92Z 0.9062
179 AAE 0.9060
180 TCV 0.9059
181 PIH 0.9050
182 V1L 0.9049
183 3ZQ 0.9049
184 8LG 0.9044
185 4XX 0.9043
186 CP2 0.9037
187 J1Z 0.9031
188 40O 0.9030
189 HSW 0.9026
190 OXE 0.9026
191 PRI 0.9021
192 280 0.9017
193 SLP 0.9016
194 JZ0 0.9013
195 2CH 0.9012
196 1DH 0.8993
197 HTS 0.8982
198 SSN 0.8980
199 VAL 0.8975
200 25T 0.8974
201 8CL 0.8972
202 2HE 0.8972
203 BAE 0.8966
204 DCD 0.8960
205 GXE 0.8958
206 TAU 0.8954
207 2HP 0.8953
208 4DX 0.8947
209 TMZ 0.8941
210 8X3 0.8937
211 URA 0.8937
212 YAN 0.8932
213 TFB 0.8928
214 H3M 0.8928
215 LG3 0.8927
216 HPY 0.8926
217 ALO 0.8924
218 DUC 0.8921
219 8GF 0.8920
220 8FH 0.8918
221 CYT 0.8911
222 KIV 0.8908
223 PRO 0.8908
224 MSF 0.8907
225 CRS 0.8907
226 26D 0.8907
227 278 0.8906
228 SGL 0.8906
229 285 0.8906
230 HHN 0.8903
231 E60 0.8901
232 FMS 0.8895
233 DTT 0.8892
234 BVG 0.8891
235 AKB 0.8887
236 POA 0.8885
237 ITU 0.8882
238 9X7 0.8882
239 LG5 0.8877
240 PRS 0.8867
241 BVF 0.8867
242 6X8 0.8866
243 TMT 0.8855
244 CNH 0.8854
245 P2D 0.8851
246 ODV 0.8848
247 2EZ 0.8843
248 DTU 0.8839
249 TTO 0.8838
250 3CH 0.8831
251 IQ0 0.8826
252 FOA 0.8816
253 RCO 0.8814
254 BVC 0.8812
255 HVQ 0.8812
256 MAK 0.8811
257 P7I 0.8796
258 ICN 0.8791
259 JBN 0.8785
260 HGQ 0.8782
261 HGW 0.8778
262 BML 0.8777
263 HCS 0.8773
264 TAN 0.8773
265 MMU 0.8770
266 2PC 0.8768
267 PYC 0.8755
268 IDH 0.8754
269 FCN 0.8754
270 D2P 0.8754
271 PAE 0.8753
272 4CH 0.8751
273 TB0 0.8751
274 HSE 0.8750
275 ICC 0.8735
276 NCM 0.8731
277 NVA 0.8730
278 T2C 0.8729
279 PUT 0.8713
280 B3R 0.8703
281 TFS 0.8702
282 1SP 0.8701
283 RSF 0.8700
284 1XX 0.8699
285 SYN 0.8689
286 1DU 0.8685
287 2MH 0.8681
288 DAB 0.8680
289 VSO 0.8679
290 RP7 0.8672
291 CP 0.8669
292 EDO 0.8665
293 CSS 0.8655
294 ECE 0.8651
295 NEQ 0.8631
296 284 0.8624
297 YHO 0.8618
298 APY 0.8610
299 MMQ 0.8603
300 WBU 0.8576
301 URF 0.8564
302 ABN 0.8556
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4IYO; Ligand: NAK; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4iyo.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4IYO; Ligand: NAK; 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: 4iyo.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4IYO; Ligand: 0JO; 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: 4iyo.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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