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 2 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 2 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 1 families.
1 4IYO - 0JO C11 H13 N2 O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; 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
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: 10
This union binding pocket(no: 1) in the query (biounit: 4iyo.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Y60 H4M 0.01136 0.4119 1.77515
2 4BLW AMP 0.02586 0.40834 2.07612
3 1M5B BN1 0.02452 0.43513 2.6616
4 5KOR GDP 0.01378 0.4198 2.77078
5 1M7Y PPG 0.01747 0.40847 3.02267
6 1KUK PCA LYS TRP 0.01243 0.42231 5.41872
7 4CT7 TRP 0.00822 0.40399 5.76132
8 4G4S LDZ 0.03019 0.40134 7.66284
9 1SOW NAD 0.02795 0.41997 8.84146
10 3R5J ACE ALA ASP VAL ALA ASA 0.03274 0.41395 9.375
Pocket No.: 2; Query (leader) PDB : 4IYO; Ligand: NAK; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4IYO; Ligand: 0JO; Similar sites found: 80
This union binding pocket(no: 3) in the query (biounit: 4iyo.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1C7O PPG 0.005491 0.4032 1.00756
2 3PDB PMP 0.0006925 0.4645 1.51134
3 3PD6 PMP 0.001144 0.4594 1.51134
4 1M32 PLP 0.02706 0.40122 1.63934
5 3K7S R52 0.008929 0.41609 1.67598
6 5G09 6DF 0.001486 0.42724 1.76322
7 4ZM4 PLP 0.009768 0.4062 1.76322
8 2TPL HPP 0.001633 0.40013 1.76322
9 4BA5 PXG 0.002735 0.42754 2.01511
10 1UU1 PMP HSA 0.0008252 0.43323 2.08955
11 5GVL GI8 0.003725 0.43526 2.267
12 5GVL PLG 0.003725 0.43526 2.267
13 4E3Q PMP 0.01806 0.40117 2.267
14 3WGC PLG 0.003326 0.40274 2.34604
15 1M1B SPV 0.00207 0.46047 2.71186
16 3F81 STT 0.02189 0.4024 2.73224
17 2ZYJ PGU 0.001882 0.43336 2.77078
18 1M7Y PPG 0.0008322 0.45347 3.02267
19 2R2N PMP 0.001885 0.44393 3.02267
20 4FL0 PLP 0.0003495 0.47854 3.27456
21 4WXG 2BO 0.001041 0.43952 3.52645
22 4RKC PMP 0.0005979 0.42658 3.52645
23 5IWQ PLP 0.001064 0.45569 3.77834
24 4JE5 PLP 0.0105 0.41266 3.77834
25 4JE5 PMP 0.01093 0.41182 3.77834
26 4F9U PBD 0.02244 0.40048 3.84615
27 2WK9 PLG 0.000004727 0.55651 3.85604
28 2WK9 PLP 0.00002318 0.5223 3.85604
29 3VP6 HLD 0.007451 0.40425 4.28212
30 1GEX PLP HSA 0.0005043 0.42271 4.49438
31 5KGS 6SR 0.01114 0.41715 4.78589
32 1MLY ACZ PLP 0.0071 0.40025 4.78589
33 3B1E P1T 0.001294 0.44682 5.35714
34 3EI9 PL6 0.001915 0.40534 5.54156
35 3CQ5 PMP 0.0001272 0.51956 5.69106
36 3LN9 FLC 0.001291 0.4736 5.7554
37 1GDE GLU PLP 0.0004684 0.4528 5.9126
38 2X5F PLP 0.0005555 0.4746 6.04534
39 1GCK ASP PLP 0.0005551 0.44533 6.75325
40 5K8B PDG 0.0004798 0.45208 6.80101
41 4ZAH T5K 0.0007633 0.40154 6.81818
42 4UHO PLP 0.01049 0.42166 7.0529
43 1LC8 33P 0.0001536 0.43656 7.14286
44 4J25 OGA 0.01751 0.41193 7.42358
45 1LW4 PLP 0.002698 0.40489 7.78098
46 1LW4 TLP 0.00483 0.40192 7.78098
47 1DFO PLG 0.0008762 0.43695 7.80856
48 5U23 TQP 0.005478 0.4185 8.11518
49 5DJ3 5DK 0.0002677 0.45489 8.24468
50 1AJS PLA 0.0008927 0.44239 8.81612
51 1WOG 16D 0.007858 0.43031 9.18033
52 4FFG 0U8 0.01891 0.40851 9.57179
53 1FC4 AKB PLP 0.000232 0.46597 10.0756
54 4K2M O1G 0.002395 0.40776 10.0756
55 5W71 9YM 0.002739 0.44242 10.5793
56 5W71 PLP 0.00136 0.42139 10.5793
57 1U08 PLP 0.0005021 0.42146 11.1399
58 2ZC0 PMP 0.0005802 0.45325 11.335
59 1UPR 4IP 0.01616 0.41404 11.3821
60 1MDZ DCS 0.001659 0.44424 11.4504
61 1MDZ PLP 0.001551 0.44424 11.4504
62 2OGA PGU 0.000449 0.45131 11.8388
63 2XBN PMP 0.00004981 0.50035 12.0907
64 2R5E QLP 0.0006555 0.44228 12.5945
65 2R5C C6P 0.0007933 0.43877 12.5945
66 3BWN PMP 0.0001123 0.45139 12.7877
67 3BWN PMP PHE 0.0004685 0.45053 12.7877
68 3E2Y PMP 0.0004886 0.4268 12.8463
69 3FRK TQP 0.002391 0.43453 13.4048
70 4LFL TG6 0.01425 0.4062 14.1975
71 1DJ9 KAM 0.0001972 0.47909 14.8438
72 1XI9 PLP 0.0003843 0.48849 14.8615
73 4R5Z PMP 0.0003796 0.44142 14.9864
74 4R5Z SIN 0.0002555 0.42509 14.9864
75 1TE2 PGA 0.02997 0.40109 15.4867
76 5LNE A2G GAL 0.02658 0.40548 15.8537
77 2HOX P1T 0.0001973 0.46901 15.869
78 1B9I PXG 0.001187 0.43707 19.5876
79 5W70 9YM 0.0005569 0.44527 23.5955
80 3ZRR PXG 0.004761 0.40583 26.8229
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