-->
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 3 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 3 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: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 KOU 1 1
2 PL6 0.761194 0.87931
3 F0G 0.738462 0.892857
4 PL5 0.69863 0.836066
5 P70 0.69863 0.894737
6 PUS 0.69863 0.791045
7 EPC 0.676923 0.857143
8 FEJ 0.676056 0.912281
9 5DK 0.671053 0.84127
10 EQJ 0.671053 0.84127
11 0JO 0.647059 0.864407
12 4LM 0.623188 0.847458
13 EVM 0.619718 0.982143
14 6DF 0.616438 0.810345
15 PLT 0.614458 0.822581
16 Z98 0.608108 0.83871
17 FEV 0.605634 0.833333
18 EXT 0.571429 0.862069
19 LLP 0.56962 0.825397
20 MET PLP 0.556962 0.761905
21 PLP 0.555556 0.836364
22 MPM 0.547945 0.844828
23 PZP 0.546875 0.839286
24 PLP PHE 0.542169 0.827586
25 AN7 0.535211 0.807018
26 HCP 0.533333 0.803279
27 P3D 0.533333 0.793651
28 FOO 0.527778 0.844828
29 PFM 0.525641 0.803279
30 PLP 999 0.525641 0.859649
31 PLP PVH 0.517241 0.746269
32 P89 0.5 0.746269
33 PLS 0.493506 0.868852
34 O1G 0.488372 0.83871
35 3QP 0.480519 0.807018
36 KET 0.475 0.85
37 PLP MYB 0.460674 0.724638
38 PP3 0.448718 0.822581
39 PDD 0.448718 0.822581
40 PDA 0.448718 0.822581
41 PLP PUT 0.444444 0.761905
42 PLR 0.439394 0.754386
43 2BK 0.4375 0.852459
44 2BO 0.4375 0.852459
45 TLP 0.4375 0.852459
46 PXP 0.434783 0.824561
47 C6P 0.432099 0.83871
48 PPD 0.432099 0.83871
49 P0P 0.428571 0.836364
50 PY5 0.426829 0.787879
51 ILP 0.416667 0.796875
52 PDG 0.416667 0.8125
53 7XF 0.416667 0.8125
54 CBA 0.416667 0.8125
55 PGU 0.416667 0.8125
56 LPI 0.411765 0.753623
57 QLP 0.411765 0.764706
58 PLG 0.410256 0.809524
59 PMP 0.408451 0.8
60 PY6 0.406977 0.764706
61 GT1 0.402778 0.737705
62 5PA 0.402439 0.8
63 ORX 0.402299 0.8
64 N5F 0.402299 0.8
Ligand no: 2; Ligand: 0JO; Similar ligands found: 64
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 LLP 0.584416 0.796875
15 PLP 0.57377 0.803571
16 AN7 0.573529 0.839286
17 P3D 0.569444 0.738462
18 PUS 0.564103 0.73913
19 PL5 0.564103 0.836066
20 P70 0.564103 0.894737
21 MPM 0.56338 0.844828
22 EQJ 0.5625 0.784615
23 5DK 0.5625 0.784615
24 HCP 0.547945 0.803279
25 P89 0.530864 0.720588
26 6DF 0.526316 0.810345
27 PLP 999 0.5 0.79661
28 PLT 0.5 0.822581
29 PFM 0.5 0.864407
30 PLP PUT 0.493506 0.707692
31 O1G 0.465116 0.753846
32 PMP 0.462687 0.714286
33 P1T 0.460526 0.828125
34 MET PLP 0.457831 0.734375
35 PLR 0.453125 0.754386
36 PLP PHE 0.448276 0.79661
37 C6P 0.443038 0.753846
38 PDA 0.441558 0.738462
39 PDD 0.441558 0.738462
40 PP3 0.441558 0.738462
41 TLP 0.43038 0.738462
42 2BK 0.43038 0.738462
43 2BO 0.43038 0.738462
44 PLS 0.43038 0.753846
45 PLP PVH 0.428571 0.720588
46 9TD 0.427083 0.728571
47 PXP 0.426471 0.704918
48 PPD 0.425 0.753846
49 PLG 0.421053 0.727273
50 P0P 0.42029 0.77193
51 PY5 0.419753 0.710145
52 PY6 0.416667 0.690141
53 GT1 0.414286 0.68254
54 PLP 142 0.410526 0.720588
55 7XF 0.409639 0.731343
56 PDG 0.409639 0.731343
57 PGU 0.409639 0.731343
58 ILP 0.409639 0.716418
59 PPG 0.409091 0.8
60 LPI 0.404762 0.680556
61 QLP 0.404762 0.690141
62 IN5 0.402597 0.707692
63 IK2 0.4 0.720588
64 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 with APoc: 144
This union binding pocket(no: 1) in the query (biounit: 4iy7.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4RJD TFP None
2 1C7O PPG 1.00756
3 3PDB PMP 1.51134
4 3PD6 PMP 1.51134
5 4ADC PLP 1.51134
6 3K7S R52 1.67598
7 6ECG PM9 1.76322
8 2X5D PLP 1.76322
9 6CD1 PLS 1.76322
10 6CD1 PLG 1.76322
11 2TPL HPP 1.76322
12 5G09 6DF 1.76322
13 4ZM4 PLP 1.76322
14 5CQG 55C 1.76322
15 3HQP FDP 1.76322
16 6EWR PMP 1.87354
17 3KVY URA 1.94175
18 6C3C EJ1 2.01511
19 4BA5 PXG 2.01511
20 3VP6 HLD 2.01511
21 1UU1 PMP HSA 2.08955
22 1VMK GUN 2.16606
23 3B4Y FLC 2.24719
24 5GVL GI8 2.267
25 5GVL PLG 2.267
26 1ZC9 PMP 2.267
27 4E3Q PMP 2.267
28 2EFJ 37T 2.34375
29 3WGC PLG 2.34604
30 6AM8 PLT 2.52525
31 4JN6 OXL 2.61438
32 1M1B SPV 2.71186
33 3F81 STT 2.73224
34 5YKT PMP 2.77078
35 2ZYJ PGU 2.77078
36 1USI PHE 2.89017
37 1II5 GLU 3.00429
38 1M7Y PPG 3.02267
39 2R2N KYN 3.02267
40 2R2N PMP 3.02267
41 2OG2 MLI 3.06407
42 1SWG BTN 3.125
43 3MBI HSX 3.13589
44 4FL0 PLP 3.27456
45 5DO8 BGC 3.27456
46 4BT5 23B 3.50195
47 4WXG 2BO 3.52645
48 4RKC PMP 3.52645
49 5VX9 FUC GAL NAG GAL BGC 3.72671
50 5IWQ PLP 3.77834
51 4JE5 PMP 3.77834
52 4JE5 PLP 3.77834
53 4B98 PXG 3.77834
54 1O69 X04 3.80711
55 3B8X G4M 3.84615
56 2WK9 PLG 3.85604
57 2WK9 PLP 3.85604
58 5WHU SIA GAL GLC 4.02685
59 5W19 9TD 4.03023
60 5WYF ILP 4.03023
61 1VCO GLN 4.28212
62 4TVD BGC 4.28212
63 1UAS GLA 4.41989
64 1GEX PLP HSA 4.49438
65 5KGS 6SR 4.78589
66 4UOX PLP 4.78589
67 1MLY ACZ PLP 4.78589
68 2DUA OXL 4.82759
69 5KOD IAC 5.03778
70 6FYQ PLP 5.03778
71 3WIR BGC 5.03778
72 1TOI HCI 5.30303
73 3EI9 PL6 5.54156
74 1Y4Z PCI 5.54156
75 1GPM CIT 5.54156
76 3CQ5 PMP 5.69106
77 3AI3 SOL 5.70342
78 3LN9 FLC 5.7554
79 4CT7 TRP 5.76132
80 1GDE GLU PLP 5.9126
81 2X5F PLP 6.04534
82 3DR4 G4M 6.13811
83 3NUB UD0 6.40669
84 5GVR LMR 6.41026
85 1GCK ASP PLP 6.75325
86 3LTW HLZ 6.78571
87 4M2K PLP 6.80101
88 5K8B PDG 6.80101
89 4ZAH T5K 6.81818
90 4UHO PLP 7.0529
91 1LC8 33P 7.14286
92 4LNL PLG 7.20721
93 4J25 OGA 7.42358
94 5FPE 3TR 7.49354
95 6DND PLP 7.55667
96 3WUR O4B 7.60234
97 1LW4 PLP 7.78098
98 1LW4 TLP 7.78098
99 1DFO PLG 7.80856
100 5U23 TQP 8.11518
101 1ELU PDA 8.20513
102 6C92 EQJ 8.24468
103 6C8T EQJ 8.24468
104 6C9B EGV 8.24468
105 1AJS PLA 8.81612
106 2PO3 T4K 9.06801
107 2XUM OGA 9.16905
108 1WOG 16D 9.18033
109 4FFG 0U8 9.57179
110 4WOH 4NP 9.63855
111 1FC4 AKB PLP 10.0756
112 4K2M O1G 10.0756
113 1LOJ URI 10.3448
114 5W71 9YM 10.5793
115 5W71 PLP 10.5793
116 1U08 PLP 11.1399
117 2ZC0 PMP 11.335
118 1MDZ PLP 11.4504
119 1MDZ DCS 11.4504
120 2OGA PGU 11.8388
121 2XBN PMP 12.0907
122 1OXO IK2 12.3426
123 2JCB ADP 12.5
124 2R5E QLP 12.5945
125 2R5C C6P 12.5945
126 3BWN PMP 12.7877
127 3BWN PMP PHE 12.7877
128 5VEQ PMP 12.8463
129 3FRK TQP 13.4048
130 2Z9V PXM 14.0306
131 4LFL TG6 14.1975
132 1DJ9 KAM 14.8438
133 1XI9 PLP 14.8615
134 2FNU PMP UD1 14.9333
135 4R5Z SIN 14.9864
136 4R5Z PMP 14.9864
137 1TE2 PGA 15.4867
138 2HOX P1T 15.869
139 4P83 U5P 15.9341
140 5TXR PLP 18.3879
141 1B9I PXG 19.5876
142 6BYF CIT 20.5882
143 5W70 9YM 23.5955
144 3ZRR PXG 26.8229
Pocket No.: 2; Query (leader) PDB : 4IY7; Ligand: 0JO; Similar sites found with APoc: 143
This union binding pocket(no: 2) in the query (biounit: 4iy7.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4RJD TFP None
2 1C7O PPG 1.00756
3 3PDB PMP 1.51134
4 3PD6 PMP 1.51134
5 4ADC PLP 1.51134
6 1M32 PLP 1.63934
7 3K7S R52 1.67598
8 6ECG PM9 1.76322
9 2X5D PLP 1.76322
10 2TPL HPP 1.76322
11 6CD1 PLS 1.76322
12 6CD1 PLG 1.76322
13 5G09 6DF 1.76322
14 5CQG 55C 1.76322
15 4ZM4 PLP 1.76322
16 3HQP FDP 1.76322
17 4U6D 3DY 1.76322
18 6EWR PMP 1.87354
19 6C3C EJ1 2.01511
20 3VP6 HLD 2.01511
21 4BA5 PXG 2.01511
22 1UU1 PMP HSA 2.08955
23 5GVL PLG 2.267
24 5GVL GI8 2.267
25 4E3Q PMP 2.267
26 4R84 CSF 2.267
27 3WGC PLG 2.34604
28 4NPL AKG 2.4
29 3FXU TSU 2.62295
30 1M1B SPV 2.71186
31 3F81 STT 2.73224
32 5YKT PMP 2.77078
33 2ZYJ PGU 2.77078
34 1USI PHE 2.89017
35 1M7Y PPG 3.02267
36 2R2N KYN 3.02267
37 6F6D AKG 3.02267
38 2R2N PMP 3.02267
39 1SWG BTN 3.125
40 4FL0 PLP 3.27456
41 5DO8 BGC 3.27456
42 4BT5 23B 3.50195
43 4WXG 2BO 3.52645
44 4RKC PMP 3.52645
45 4UP4 GAL NAG 3.52645
46 5VX9 FUC GAL NAG GAL BGC 3.72671
47 5IWQ PLP 3.77834
48 4JE5 PLP 3.77834
49 4JE5 PMP 3.77834
50 4B98 PXG 3.77834
51 1O69 X04 3.80711
52 3B8X G4M 3.84615
53 2WK9 PLG 3.85604
54 2WK9 PLP 3.85604
55 5WHU SIA GAL GLC 4.02685
56 5W19 9TD 4.03023
57 5WYF ILP 4.03023
58 1VCO GLN 4.28212
59 5O42 NAD 4.37956
60 5O42 BGC 4.37956
61 5O42 9JW 4.37956
62 5LNW HG3 4.43038
63 1GEX PLP HSA 4.49438
64 5KGS 6SR 4.78589
65 4UOX PLP 4.78589
66 1MLY ACZ PLP 4.78589
67 2DUA OXL 4.82759
68 6FYQ PLP 5.03778
69 1TOI HCI 5.30303
70 3EI9 PL6 5.54156
71 1Y4Z PCI 5.54156
72 1GPM CIT 5.54156
73 3CQ5 PMP 5.69106
74 3AI3 SOL 5.70342
75 3LN9 FLC 5.7554
76 4CT7 TRP 5.76132
77 1GDE GLU PLP 5.9126
78 2X5F PLP 6.04534
79 3DR4 G4M 6.13811
80 3NUB UD0 6.40669
81 5GVR LMR 6.41026
82 5OJI NAP 6.53846
83 5OJI ISN 6.53846
84 1GCK ASP PLP 6.75325
85 3LTW HLZ 6.78571
86 4M2K PLP 6.80101
87 5K8B PDG 6.80101
88 4ZAH T5K 6.81818
89 4UHO PLP 7.0529
90 1LC8 33P 7.14286
91 4LNL PLG 7.20721
92 4J25 OGA 7.42358
93 5FPE 3TR 7.49354
94 6DND PLP 7.55667
95 3WUR O4B 7.60234
96 2HJ9 AI2 7.66962
97 1LW4 PLP 7.78098
98 1LW4 TLP 7.78098
99 1DFO PLG 7.80856
100 5U23 TQP 8.11518
101 3EW2 BTN 8.14815
102 1ELU PDA 8.20513
103 6C92 EQJ 8.24468
104 6C8T EQJ 8.24468
105 6C9B EGV 8.24468
106 1AJS PLA 8.81612
107 2PO3 T4K 9.06801
108 1WOG 16D 9.18033
109 4FFG 0U8 9.57179
110 1FC4 AKB PLP 10.0756
111 4K2M O1G 10.0756
112 1LOJ URI 10.3448
113 5W71 9YM 10.5793
114 5W71 PLP 10.5793
115 1U08 PLP 11.1399
116 2ZC0 PMP 11.335
117 1UPR 4IP 11.3821
118 1MDZ PLP 11.4504
119 1MDZ DCS 11.4504
120 2OGA PGU 11.8388
121 2XBN PMP 12.0907
122 1OXO IK2 12.3426
123 2R5E QLP 12.5945
124 2R5C C6P 12.5945
125 3BWN PMP 12.7877
126 3BWN PMP PHE 12.7877
127 5VEQ PMP 12.8463
128 3FRK TQP 13.4048
129 2Z9V PXM 14.0306
130 4LFL TG6 14.1975
131 1DJ9 KAM 14.8438
132 1XI9 PLP 14.8615
133 2FNU PMP UD1 14.9333
134 4R5Z SIN 14.9864
135 4R5Z PMP 14.9864
136 5LNE A2G GAL 15.8537
137 2HOX P1T 15.869
138 4P83 U5P 15.9341
139 5TXR PLP 18.3879
140 1B9I PXG 19.5876
141 6BYF CIT 20.5882
142 5W70 9YM 23.5955
143 3ZRR PXG 26.8229
Pocket No.: 3; Query (leader) PDB : 4IY7; Ligand: KOU; Similar sites found with APoc: 20
This union binding pocket(no: 3) in the query (biounit: 4iy7.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1M32 PLP 1.63934
2 2YBP 2HG 2.09974
3 1A99 PUT 2.61628
4 2WSB NAD 2.75591
5 1KQR MNA 2.7933
6 2P3I MNA 3.10559
7 4EKV BTN 3.14465
8 3RDO BTN 3.26797
9 4RW3 DKA 3.31126
10 5O42 NAD 4.37956
11 5O42 BGC 4.37956
12 5O42 9JW 4.37956
13 5GWT SIN 4.67626
14 5XQW 8EU 5.21327
15 5OJI NAP 6.53846
16 5OJI ISN 6.53846
17 1WHT BZS 6.64062
18 2HJ9 AI2 7.66962
19 4R8L ASP 8.31169
20 1RJW ETF 10.0295
Pocket No.: 4; Query (leader) PDB : 4IY7; Ligand: KOU; Similar sites found with APoc: 14
This union binding pocket(no: 4) in the query (biounit: 4iy7.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2O1C PPV None
2 6BKK 308 None
3 1FH8 XYP XIF 2.24359
4 3VMW ADA ADA ADA 2.45399
5 3BY9 SIN 2.69231
6 3COB ADP 2.71003
7 5VFC 9BA 3.85852
8 5LNW HG3 4.43038
9 2Z4T C5P 4.78589
10 5G3R 89A 5.39773
11 1ZPD CIT 6.04534
12 3WJO IPE 7.12166
13 4GGZ BTN 11.3043
14 4Z28 BTN 15.6716
APoc FAQ
Feedback