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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 3 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 3 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
Ligand no: 1; 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
Ligand no: 2; Ligand: NAK; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 NAK 1 1
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: 29
This union binding pocket(no: 1) in the query (biounit: 4iyo.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 6BXO SAH 1.52905
2 4X3R 686 1.76322
3 5GWE GWM 1.76322
4 1Y60 H4M 1.77515
5 4BLW AMP 2.07612
6 2ZB4 NAP 2.52101
7 2ZB4 5OP 2.52101
8 1M5B BN1 2.6616
9 5KOR GDP 2.77078
10 1QXO FMN 2.77078
11 1M7Y PPG 3.02267
12 5FTB ANP 3.52645
13 2IO8 ADP 4.03023
14 2IYA UDP 4.03023
15 4POO SAM 4.5
16 2ZZV LAC 5.26316
17 1KUK PCA LYS TRP 5.41872
18 5X2N ALA 5.52995
19 2AMT 1AA 5.66038
20 5OHJ 9VE 5.70071
21 4CT7 TRP 5.76132
22 1U1I NAD 5.79345
23 4PLT NAI 6.94864
24 1LC8 33P 7.14286
25 4G4S LDZ 7.66284
26 1SOW NAD 8.84146
27 2YG3 FAD 9.3199
28 3R5J ACE ALA ASP VAL ALA ASA 9.375
29 3K5I ADP 17.1216
Pocket No.: 2; Query (leader) PDB : 4IYO; Ligand: NAK; Similar sites found with APoc: 25
This union binding pocket(no: 2) in the query (biounit: 4iyo.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 1PI5 SM2 1.39665
2 1CT9 GLN 1.51134
3 4I6G FAD 1.76322
4 5JFT ACE ASP GLU VAL ASP 0QE 2.40964
5 1PZG A3D 2.51889
6 6GNA FAD 2.77778
7 2H04 4UN 2.8754
8 6H21 UD1 3.27456
9 3LXK MI1 3.66972
10 4NU0 AP5 3.68664
11 3A25 SAM 3.98671
12 4LTN FMN 4.56853
13 4LTN NAI 4.56853
14 6EQS BV8 4.72727
15 2GRU NAD 5.43478
16 2HJR APR 6.09756
17 1GUZ NAD 6.12903
18 4MKG AP5 6.45161
19 4PLT OXM 6.94864
20 3K05 SEP GLN GLU TYR NH2 7
21 3EUF BAU 7.92683
22 4WOH 4NP 9.63855
23 4GUS FAD 11.2903
24 1YP1 LYS ASN LEU 11.3861
25 5A4W QCT 20.283
Pocket No.: 3; Query (leader) PDB : 4IYO; Ligand: 0JO; Similar sites found with APoc: 152
This union binding pocket(no: 3) in the query (biounit: 4iyo.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2O1C PPV None
2 4RJD TFP None
3 1C7O PPG 1.00756
4 6HDT BTN 1.50376
5 3PDB PMP 1.51134
6 3PD6 PMP 1.51134
7 4ADC PLP 1.51134
8 1M32 PLP 1.63934
9 3K7S R52 1.67598
10 6ECG PM9 1.76322
11 2X5D PLP 1.76322
12 2TPL HPP 1.76322
13 6CD1 PLS 1.76322
14 6CD1 PLG 1.76322
15 5G09 6DF 1.76322
16 5CQG 55C 1.76322
17 4ZM4 PLP 1.76322
18 3HQP FDP 1.76322
19 5HV7 RBL 1.76322
20 5O2N FLC 1.78571
21 6EWR PMP 1.87354
22 6C3C EJ1 2.01511
23 4BA5 PXG 2.01511
24 1UU1 PMP HSA 2.08955
25 1FH8 XYP XIF 2.24359
26 5GVL GI8 2.267
27 5GVL PLG 2.267
28 4E3Q PMP 2.267
29 2EFJ 37T 2.34375
30 3WGC PLG 2.34604
31 4NPL AKG 2.4
32 3COB ADP 2.71003
33 1M1B SPV 2.71186
34 3F81 STT 2.73224
35 5YKT PMP 2.77078
36 2ZYJ PGU 2.77078
37 1USI PHE 2.89017
38 1II5 GLU 3.00429
39 1M7Y PPG 3.02267
40 2R2N PMP 3.02267
41 2R2N KYN 3.02267
42 1SWG BTN 3.125
43 4FL0 PLP 3.27456
44 5DO8 BGC 3.27456
45 3A8U PLP 3.34076
46 4BT5 23B 3.50195
47 4RKC PMP 3.52645
48 4WXG 2BO 3.52645
49 5VX9 FUC GAL NAG GAL BGC 3.72671
50 5IWQ PLP 3.77834
51 4JE5 PLP 3.77834
52 4B98 PXG 3.77834
53 4JE5 PMP 3.77834
54 1O69 X04 3.80711
55 3B8X G4M 3.84615
56 4F9U PBD 3.84615
57 2WK9 PLG 3.85604
58 2WK9 PLP 3.85604
59 5WHU SIA GAL GLC 4.02685
60 5W19 9TD 4.03023
61 5WYF ILP 4.03023
62 3VP6 HLD 4.28212
63 5LNW HG3 4.43038
64 1GEX PLP HSA 4.49438
65 6GPC ARG 4.7619
66 5KGS 6SR 4.78589
67 4UOX PLP 4.78589
68 1MLY ACZ PLP 4.78589
69 2DUA OXL 4.82759
70 1NSZ GLC 4.89914
71 6FYQ PLP 5.03778
72 3WIR BGC 5.03778
73 1TOI HCI 5.30303
74 3EI9 PL6 5.54156
75 1Y4Z PCI 5.54156
76 1GPM CIT 5.54156
77 3CQ5 PMP 5.69106
78 3AI3 SOL 5.70342
79 3LN9 FLC 5.7554
80 1GDE GLU PLP 5.9126
81 2X5F PLP 6.04534
82 1ZPD CIT 6.04534
83 3DR4 G4M 6.13811
84 3NUB UD0 6.40669
85 5GVR LMR 6.41026
86 5OJI ISN 6.53846
87 5OJI NAP 6.53846
88 5X20 AOT 6.73077
89 1GCK ASP PLP 6.75325
90 3LTW HLZ 6.78571
91 4M2K PLP 6.80101
92 5K8B PDG 6.80101
93 4ZAH T5K 6.81818
94 4UHO PLP 7.0529
95 1LC8 33P 7.14286
96 4LNL PLG 7.20721
97 4J25 OGA 7.42358
98 5FPE 3TR 7.49354
99 6DND PLP 7.55667
100 3WUR O4B 7.60234
101 1LW4 PLP 7.78098
102 1LW4 TLP 7.78098
103 1DFO PLG 7.80856
104 5U23 TQP 8.11518
105 3EW2 BTN 8.14815
106 1ELU PDA 8.20513
107 6C92 EQJ 8.24468
108 6C8T EQJ 8.24468
109 6C9B EGV 8.24468
110 1AJS PLA 8.81612
111 6CI9 F3V 8.88031
112 2PO3 T4K 9.06801
113 1WOG 16D 9.18033
114 4FFG 0U8 9.57179
115 4WOH 4NP 9.63855
116 1RJW ETF 10.0295
117 1FC4 AKB PLP 10.0756
118 4K2M O1G 10.0756
119 1LOJ URI 10.3448
120 5W71 9YM 10.5793
121 5W71 PLP 10.5793
122 1U08 PLP 11.1399
123 2ZC0 PMP 11.335
124 1UPR 4IP 11.3821
125 1MDZ PLP 11.4504
126 1MDZ DCS 11.4504
127 2OGA PGU 11.8388
128 2XBN PMP 12.0907
129 1OXO IK2 12.3426
130 2R5E QLP 12.5945
131 2R5C C6P 12.5945
132 3BWN PMP 12.7877
133 3BWN PMP PHE 12.7877
134 5VEQ PMP 12.8463
135 3FRK TQP 13.4048
136 2Z9V PXM 14.0306
137 4LFL TG6 14.1975
138 1DJ9 KAM 14.8438
139 1XI9 PLP 14.8615
140 2FNU PMP UD1 14.9333
141 4R5Z SIN 14.9864
142 4R5Z PMP 14.9864
143 1TE2 PGA 15.4867
144 5LNE A2G GAL 15.8537
145 2HOX P1T 15.869
146 4P83 U5P 15.9341
147 3AJ4 SEP 16.0714
148 5TXR PLP 18.3879
149 1B9I PXG 19.5876
150 6BYF CIT 20.5882
151 5W70 9YM 23.5955
152 3ZRR PXG 26.8229
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