Receptor
PDB id Resolution Class Description Source Keywords
4IY7 1.7 Å EC: 4.4.1.1 CRYSTAL STRUCTURE OF CYSTATHIONINE GAMMA LYASE (XOMETC) FROM XANTHOMONAS ORYZAE PV. ORYZAE IN COMPLEX WITH E-SITE SERINEE XTERNAL ALDIMINE STRUCTURE WITH SERINE AND A-SITE EXTERNALST RUCTURE WITH AMINOACRYLATE INTERMEDIATES XANTHOMONAS ORYZAE PV. ORYZAE XOCGL SERINE EXTERNAL SCHIFF BASE AMINOACRYLATE EXTERNAL SBASE PLP DEPENDENT ENZYME LYASE CYS-MET METABOLISM PLP DENZYME CYSTATHIONINE GAMMA LYASE PLP BINDING
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
PYR D:402;
B:402;
Invalid;
Invalid;
none;
none;
submit data
88.062 C3 H4 O3 CC(=O...
GOL A:403;
A:402;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
KOU B:403;
C:402;
D:403;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
334.219 C11 H15 N2 O8 P Cc1c(...
0JO A:405;
Valid;
none;
submit data
316.204 C11 H13 N2 O7 P Cc1c(...
SO4 A:404;
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
4IY7 1.7 Å EC: 4.4.1.1 CRYSTAL STRUCTURE OF CYSTATHIONINE GAMMA LYASE (XOMETC) FROM XANTHOMONAS ORYZAE PV. ORYZAE IN COMPLEX WITH E-SITE SERINEE XTERNAL ALDIMINE STRUCTURE WITH SERINE AND A-SITE EXTERNALST RUCTURE WITH AMINOACRYLATE INTERMEDIATES XANTHOMONAS ORYZAE PV. ORYZAE XOCGL SERINE EXTERNAL SCHIFF BASE AMINOACRYLATE EXTERNAL SBASE PLP DEPENDENT ENZYME LYASE CYS-MET METABOLISM PLP DENZYME CYSTATHIONINE GAMMA LYASE PLP BINDING
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 2 families.
1 4IY7 - KOU C11 H15 N2 O8 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 2 families.
1 4IY7 - KOU C11 H15 N2 O8 P Cc1c(c(c(c....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3VK3 - MET C5 H11 N O2 S CSCC[C@@H]....
2 5X2X - 4LM C12 H15 N2 O7 P C/C=C(C(=O....
3 5X2Z - 3LM C13 H19 N2 O7 P S Cc1c(c(c(c....
4 1E5F - PLP C8 H10 N O6 P Cc1c(c(c(c....
5 4IY7 - KOU C11 H15 N2 O8 P Cc1c(c(c(c....
6 5M3Z Ki = 0.6 mM NLE C6 H13 N O2 CCCC[C@@H]....
7 4HF8 - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
8 3MKJ - PZP C8 H11 N2 O5 P [H]/N=C/c1....
9 4OMA - LCS C11 H14 N3 O7 P Cc1c(c(c(c....
10 1CL2 - PPG C14 H20 N3 O8 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: KOU; Similar ligands found: 56
No: Ligand ECFP6 Tc MDL keys Tc
1 KOU 1 1
2 PL6 0.761194 0.87931
3 PUS 0.69863 0.791045
4 PL5 0.69863 0.836066
5 EPC 0.676923 0.857143
6 5DK 0.671053 0.84127
7 0JO 0.647059 0.864407
8 4LM 0.623188 0.847458
9 6DF 0.616438 0.810345
10 PLT 0.614458 0.822581
11 Z98 0.608108 0.83871
12 EXT 0.571429 0.862069
13 LLP 0.56962 0.825397
14 PLP 0.555556 0.836364
15 MPM 0.547945 0.844828
16 PZP 0.546875 0.839286
17 PLP PHE 0.542169 0.827586
18 AN7 0.535211 0.807018
19 P3D 0.533333 0.793651
20 HCP 0.533333 0.803279
21 FOO 0.527778 0.844828
22 PFM 0.525641 0.803279
23 PLP PVH 0.517241 0.746269
24 P89 0.5 0.746269
25 PLS 0.493506 0.868852
26 O1G 0.488372 0.83871
27 3QP 0.480519 0.807018
28 KET 0.475 0.85
29 PLP ABU 0.469136 0.8
30 PLP PUT 0.4625 0.75
31 PLP MYB 0.460674 0.724638
32 PP3 0.448718 0.822581
33 PDD 0.448718 0.822581
34 PDA 0.448718 0.822581
35 PLR 0.439394 0.754386
36 2BK 0.4375 0.852459
37 TLP 0.4375 0.852459
38 2BO 0.4375 0.852459
39 PXP 0.434783 0.824561
40 C6P 0.432099 0.83871
41 PPD 0.432099 0.83871
42 P0P 0.428571 0.836364
43 PY5 0.426829 0.787879
44 7XF 0.416667 0.8125
45 CBA 0.416667 0.8125
46 ILP 0.416667 0.796875
47 PDG 0.416667 0.8125
48 PGU 0.416667 0.8125
49 QLP 0.411765 0.764706
50 PLG 0.410256 0.809524
51 PMP 0.408451 0.8
52 PY6 0.406977 0.764706
53 GT1 0.402778 0.737705
54 5PA 0.402439 0.8
55 ORX 0.402299 0.8
56 N5F 0.402299 0.8
Ligand no: 2; Ligand: 0JO; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 0JO 1 1
2 4LM 0.71875 0.946429
3 KOU 0.647059 0.864407
4 Z98 0.625 0.809524
5 EXT 0.61194 0.830508
6 PL6 0.611111 0.87931
7 EPC 0.597015 0.857143
8 PZP 0.590164 0.807018
9 FOO 0.588235 0.877193
10 LLP 0.584416 0.796875
11 PLP 0.57377 0.803571
12 AN7 0.573529 0.839286
13 P3D 0.569444 0.738462
14 PUS 0.564103 0.73913
15 PL5 0.564103 0.836066
16 MPM 0.56338 0.844828
17 5DK 0.5625 0.784615
18 HCP 0.547945 0.803279
19 P89 0.530864 0.720588
20 6DF 0.526316 0.810345
21 PLP ABU 0.519481 0.770492
22 PLP PUT 0.513158 0.721311
23 PFM 0.5 0.864407
24 PLT 0.5 0.822581
25 O1G 0.465116 0.753846
26 PMP 0.462687 0.714286
27 P1T 0.460526 0.828125
28 PLR 0.453125 0.754386
29 PLP PHE 0.448276 0.79661
30 C6P 0.443038 0.753846
31 PP3 0.441558 0.738462
32 PDD 0.441558 0.738462
33 PDA 0.441558 0.738462
34 2BK 0.43038 0.738462
35 2BO 0.43038 0.738462
36 PLS 0.43038 0.753846
37 TLP 0.43038 0.738462
38 PLP PVH 0.428571 0.720588
39 PXP 0.426471 0.704918
40 PPD 0.425 0.753846
41 PLG 0.421053 0.727273
42 P0P 0.42029 0.77193
43 PY5 0.419753 0.710145
44 PY6 0.416667 0.690141
45 GT1 0.414286 0.68254
46 PLP 142 0.410526 0.720588
47 PGU 0.409639 0.731343
48 7XF 0.409639 0.731343
49 ILP 0.409639 0.716418
50 PDG 0.409639 0.731343
51 PPG 0.409091 0.8
52 QLP 0.404762 0.690141
53 IN5 0.402597 0.707692
54 IK2 0.4 0.720588
55 HEY 0.4 0.761194
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4IY7; Ligand: KOU; Similar sites found: 78
This union binding pocket(no: 1) in the query (biounit: 4iy7.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1C7O PPG 0.005731 0.40241 1.00756
2 3PDB PMP 0.000713 0.42034 1.51134
3 3PD6 PMP 0.001322 0.4067 1.51134
4 4ADC PLP 0.01423 0.40231 1.51134
5 5G09 6DF 0.00123 0.43071 1.76322
6 2TPL HPP 0.00203 0.43036 1.76322
7 5CQG 55C 0.008806 0.42267 1.76322
8 4ZM4 PLP 0.007201 0.41234 1.76322
9 4BA5 PXG 0.00227 0.4312 2.01511
10 3VP6 HLD 0.007826 0.40333 2.01511
11 1UU1 PMP HSA 0.000749 0.44186 2.08955
12 5GVL GI8 0.003235 0.43806 2.267
13 5GVL PLG 0.003235 0.43806 2.267
14 1ZC9 PMP 0.001647 0.42132 2.267
15 3WGC PLG 0.002933 0.4047 2.34604
16 2ZYJ PGU 0.001527 0.43733 2.77078
17 1M7Y PPG 0.0008643 0.45274 3.02267
18 2R2N PMP 0.00195 0.44324 3.02267
19 3MBI HSX 0.01968 0.40334 3.13589
20 4FL0 PLP 0.0003783 0.42982 3.27456
21 4RKC PMP 0.0007285 0.45833 3.52645
22 4WXG 2BO 0.001067 0.41802 3.52645
23 5IWQ PLP 0.0007487 0.4629 3.77834
24 4JE5 PMP 0.009218 0.41542 3.77834
25 4JE5 PLP 0.009331 0.41516 3.77834
26 4B98 PXG 0.004082 0.40171 3.77834
27 3B8X G4M 0.0003511 0.47584 3.84615
28 2WK9 PLG 0.000005608 0.5532 3.85604
29 2WK9 PLP 0.00002655 0.5197 3.85604
30 5WYF ILP 0.005887 0.40192 4.03023
31 4TVD BGC 0.01895 0.41034 4.28212
32 1GEX PLP HSA 0.0004581 0.45847 4.49438
33 5KGS 6SR 0.00902 0.42141 4.78589
34 1MLY ACZ PLP 0.005464 0.40511 4.78589
35 5KOD IAC 0.005819 0.41472 5.03778
36 3B1E P1T 0.001132 0.41522 5.35714
37 3EI9 PL6 0.002031 0.40834 5.54156
38 3CQ5 PMP 0.0001261 0.42963 5.69106
39 1GDE GLU PLP 0.0004206 0.44587 5.9126
40 2X5F PLP 0.0005066 0.41376 6.04534
41 3DR4 G4M 0.0003465 0.48125 6.13811
42 1GCK ASP PLP 0.0005723 0.44477 6.75325
43 5K8B PDG 0.0005024 0.45122 6.80101
44 4ZAH T5K 0.0008349 0.40096 6.81818
45 4UHO PLP 0.0123 0.41811 7.0529
46 1LC8 33P 0.0001527 0.48102 7.14286
47 1LW4 PLP 0.002448 0.40458 7.78098
48 1LW4 TLP 0.004882 0.4017 7.78098
49 1DFO PLG 0.0007795 0.4391 7.80856
50 5U23 TQP 0.0049 0.42066 8.11518
51 5DJ3 5DK 0.0002388 0.45684 8.24468
52 1AJS PLA 0.001027 0.43976 8.81612
53 2PO3 T4K 0.001236 0.45125 9.06801
54 1FC4 AKB PLP 0.0002337 0.45679 10.0756
55 4K2M O1G 0.002209 0.42369 10.0756
56 5W71 9YM 0.003065 0.44018 10.5793
57 5W71 PLP 0.001272 0.42291 10.5793
58 1U08 PLP 0.0004869 0.42218 11.1399
59 2ZC0 PMP 0.0005047 0.43984 11.335
60 1MDZ DCS 0.001785 0.44282 11.4504
61 1MDZ PLP 0.001669 0.44282 11.4504
62 2OGA PGU 0.0004132 0.45285 11.8388
63 2XBN PMP 0.00006319 0.49586 12.0907
64 2R5E QLP 0.0006106 0.44358 12.5945
65 2R5C C6P 0.000804 0.43853 12.5945
66 3BWN PMP PHE 0.0004328 0.452 12.7877
67 3BWN PMP 0.0001017 0.45117 12.7877
68 3E2Y PMP 0.0004289 0.42913 12.8463
69 3FRK TQP 0.002136 0.43671 13.4048
70 1DJ9 KAM 0.0001931 0.4795 14.8438
71 1XI9 PLP 0.0004961 0.41512 14.8615
72 2FNU PMP UD1 0.000317 0.48049 14.9333
73 4R5Z PMP 0.0003576 0.44005 14.9864
74 4R5Z SIN 0.0002549 0.42485 14.9864
75 2HOX P1T 0.0001831 0.4613 15.869
76 1B9I PXG 0.001318 0.43511 19.5876
77 5W70 9YM 0.0005019 0.44718 23.5955
78 3ZRR PXG 0.003896 0.40952 26.8229
Pocket No.: 2; Query (leader) PDB : 4IY7; Ligand: 0JO; Similar sites found: 75
This union binding pocket(no: 2) in the query (biounit: 4iy7.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1C7O PPG 0.005924 0.40181 1.00756
2 3PDB PMP 0.0006974 0.42042 1.51134
3 3PD6 PMP 0.001215 0.40789 1.51134
4 4ADC PLP 0.01236 0.40521 1.51134
5 2TPL HPP 0.001563 0.4353 1.76322
6 5G09 6DF 0.001264 0.43022 1.76322
7 5CQG 55C 0.008357 0.42322 1.76322
8 4ZM4 PLP 0.008102 0.40997 1.76322
9 4BA5 PXG 0.002263 0.43126 2.01511
10 3VP6 HLD 0.006968 0.40552 2.01511
11 1UU1 PMP HSA 0.0008013 0.44061 2.08955
12 5GVL PLG 0.003657 0.43563 2.267
13 5GVL GI8 0.003657 0.43563 2.267
14 3WGC PLG 0.00303 0.40428 2.34604
15 2ZYJ PGU 0.001849 0.4337 2.77078
16 1M7Y PPG 0.0008025 0.45417 3.02267
17 2R2N PMP 0.001893 0.44385 3.02267
18 4FL0 PLP 0.0003465 0.43191 3.27456
19 4RKC PMP 0.0006706 0.45999 3.52645
20 4WXG 2BO 0.001192 0.41631 3.52645
21 4UP4 GAL NAG 0.0356 0.40153 3.52645
22 5IWQ PLP 0.001013 0.45669 3.77834
23 4JE5 PLP 0.009728 0.41428 3.77834
24 4JE5 PMP 0.01017 0.41335 3.77834
25 4B98 PXG 0.003918 0.40218 3.77834
26 3B8X G4M 0.0003344 0.47679 3.84615
27 2WK9 PLG 0.000004555 0.55723 3.85604
28 2WK9 PLP 0.00002158 0.52367 3.85604
29 1GEX PLP HSA 0.0005004 0.4568 4.49438
30 5KGS 6SR 0.009233 0.42094 4.78589
31 1MLY ACZ PLP 0.005918 0.40363 4.78589
32 3B1E P1T 0.001306 0.41299 5.35714
33 3EI9 PL6 0.001915 0.40926 5.54156
34 3CQ5 PMP 0.0001041 0.43185 5.69106
35 1GDE GLU PLP 0.0004457 0.44476 5.9126
36 2X5F PLP 0.0005786 0.41191 6.04534
37 3DR4 G4M 0.0003605 0.48046 6.13811
38 1GCK ASP PLP 0.0006342 0.44288 6.75325
39 5K8B PDG 0.0005698 0.44889 6.80101
40 4ZAH T5K 0.0008373 0.40079 6.81818
41 4UHO PLP 0.01018 0.42233 7.0529
42 1LC8 33P 0.000164 0.47966 7.14286
43 1LW4 PLP 0.002413 0.4067 7.78098
44 1LW4 TLP 0.004042 0.40497 7.78098
45 1DFO PLG 0.0007945 0.43874 7.80856
46 5U23 TQP 0.005536 0.4183 8.11518
47 5DJ3 5DK 0.0002795 0.45414 8.24468
48 1AJS PLA 0.0008816 0.44262 8.81612
49 2PO3 T4K 0.001396 0.44888 9.06801
50 1FC4 AKB PLP 0.0002447 0.4559 10.0756
51 4K2M O1G 0.002472 0.4216 10.0756
52 5W71 9YM 0.00291 0.44121 10.5793
53 5W71 PLP 0.001342 0.42165 10.5793
54 1U08 PLP 0.0005207 0.42082 11.1399
55 2ZC0 PMP 0.0005458 0.43752 11.335
56 1MDZ PLP 0.001636 0.44321 11.4504
57 1MDZ DCS 0.001826 0.44238 11.4504
58 2OGA PGU 0.0004891 0.44973 11.8388
59 2XBN PMP 0.00005357 0.49898 12.0907
60 2R5E QLP 0.0006565 0.44225 12.5945
61 2R5C C6P 0.0007912 0.43882 12.5945
62 3BWN PMP PHE 0.0004202 0.45254 12.7877
63 3BWN PMP 0.000105 0.45081 12.7877
64 3E2Y PMP 0.0004699 0.42741 12.8463
65 3FRK TQP 0.002483 0.4338 13.4048
66 1DJ9 KAM 0.000209 0.47796 14.8438
67 1XI9 PLP 0.0003297 0.41842 14.8615
68 2FNU PMP UD1 0.0003635 0.4778 14.9333
69 4R5Z PMP 0.0003445 0.44181 14.9864
70 4R5Z SIN 0.000243 0.42421 14.9864
71 5LNE A2G GAL 0.02483 0.40684 15.8537
72 2HOX P1T 0.0001725 0.46216 15.869
73 1B9I PXG 0.001237 0.43629 19.5876
74 5W70 9YM 0.0005088 0.44693 23.5955
75 3ZRR PXG 0.0044 0.40728 26.8229
Pocket No.: 3; Query (leader) PDB : 4IY7; Ligand: KOU; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4iy7.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4IY7; Ligand: KOU; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4iy7.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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