Receptor
PDB id Resolution Class Description Source Keywords
1U08 2.35 Å EC: 2.6.1.- CRYSTAL STRUCTURE AND REACTIVITY OF YBDL FROM ESCHERICHIA CO IDENTIFY A METHIONINE AMINOTRANSFERASE FUNCTION. ESCHERICHIA COLI ALPHA BETA PROTEIN TRANSFERASE
Ref.: CRYSTAL STRUCTURE AND REACTIVITY OF YBDL FROM ESCHE COLI IDENTIFY A METHIONINE AMINOTRANSFERASE FUNCTIO FEBS LETT. V. 571 141 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLP A:400;
B:1400;
Valid;
Valid;
none;
none;
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247.142 C8 H10 N O6 P Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1U08 2.35 Å EC: 2.6.1.- CRYSTAL STRUCTURE AND REACTIVITY OF YBDL FROM ESCHERICHIA CO IDENTIFY A METHIONINE AMINOTRANSFERASE FUNCTION. ESCHERICHIA COLI ALPHA BETA PROTEIN TRANSFERASE
Ref.: CRYSTAL STRUCTURE AND REACTIVITY OF YBDL FROM ESCHE COLI IDENTIFY A METHIONINE AMINOTRANSFERASE FUNCTIO FEBS LETT. V. 571 141 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1U08 - PLP C8 H10 N O6 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 5 families.
1 1U08 - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1GDE - GLU PLP n/a n/a
2 1V2F - HCI C9 H10 O2 c1ccc(cc1)....
3 1U08 - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 1GCK - ASP PLP n/a n/a
5 1XI9 - PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLP; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 MPM 0.564516 0.814815
12 KOU 0.555556 0.836364
13 HCP 0.546875 0.77193
14 6DF 0.545455 0.811321
15 PXL 0.541667 0.659574
16 Z98 0.537313 0.75
17 PXP 0.537037 0.862745
18 PMP 0.527273 0.767857
19 P0P 0.527273 0.916667
20 PL6 0.522388 0.818182
21 GT1 0.517857 0.830189
22 PFM 0.514706 0.803571
23 LLP 0.5 0.737705
24 PL5 0.479452 0.775862
25 PUS 0.479452 0.707692
26 MPL 0.473684 0.836364
27 PLG 0.46875 0.75
28 IN5 0.46875 0.758621
29 P89 0.466667 0.714286
30 PLP PUT 0.463768 0.684211
31 5DK 0.460526 0.725806
32 O1G 0.454545 0.75
33 PLP ABU 0.450704 0.706897
34 PLT 0.439024 0.762712
35 X04 0.431034 0.851852
36 PP3 0.426471 0.762712
37 P1T 0.426471 0.714286
38 PDD 0.426471 0.762712
39 PDA 0.426471 0.762712
40 IK2 0.42029 0.714286
41 33P 0.42029 0.745763
42 2BO 0.414286 0.793103
43 PLS 0.414286 0.779661
44 PMH 0.414286 0.619718
45 5PA 0.414286 0.714286
46 TLP 0.414286 0.793103
47 2BK 0.414286 0.793103
48 C6P 0.408451 0.75
49 PPD 0.408451 0.75
50 QLP 0.405405 0.681818
51 MP5 0.403509 0.666667
52 PY5 0.402778 0.703125
53 PLA 0.402778 0.703125
54 HEY 0.4 0.703125
55 PLP PHE 0.4 0.732143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1U08; Ligand: PLP; Similar sites found: 94
This union binding pocket(no: 1) in the query (biounit: 1u08.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3MVH WFE 0.0316 0.40052 1.16959
2 5K8B PDG 0.0001544 0.50586 1.29534
3 3ZL8 ADP 0.005659 0.42572 1.29534
4 1MLY ACZ PLP 0.004848 0.4308 1.81347
5 1VJ7 GDP 0.008967 0.41449 1.81347
6 3WGC PLG 0.0001318 0.49754 2.05279
7 5GVL GI8 0.004004 0.45782 2.07254
8 5GVL PLG 0.004004 0.45782 2.07254
9 4ZSY RW2 0.0006272 0.40927 2.07254
10 1PMO PLR 0.0004782 0.46569 2.33161
11 4LNL PLG 0.0001046 0.49958 2.4024
12 4LNL 2BO 0.0001452 0.49553 2.4024
13 2Z9V PXM 0.0001414 0.50133 2.59067
14 2FYF PLP 0.0005391 0.46637 2.59067
15 2G50 PYR 0.002582 0.44264 2.84974
16 3FQ8 PMP 0.006281 0.42868 2.84974
17 1LW4 TLP 0.0001944 0.49441 2.88184
18 1LW4 PLP 0.0001614 0.49335 2.88184
19 3ITJ CIT 0.02001 0.40587 2.95858
20 3BWN PMP 0.0000000449 0.63187 3.10881
21 3BWN PMP PHE 0.0000002727 0.5215 3.10881
22 4E1O PLP PVH 0.01271 0.41198 3.10881
23 2OGA PGU 0.0007041 0.47165 3.36788
24 4NES UDP 0.003252 0.43339 3.47594
25 5W70 9YM 0.0001718 0.4993 3.62694
26 1FC4 AKB PLP 0.0001637 0.43883 3.62694
27 4IP7 FLC 0.01127 0.40767 3.88601
28 4OKS 2T9 0.009849 0.40589 3.88601
29 4ADC PLP 0.005968 0.40521 3.88601
30 4EXO PYR 0.02256 0.40301 4.10959
31 5IWQ PLP 0.000004081 0.54708 4.14508
32 5WYF ILP 0.002215 0.44548 4.14508
33 1VJO PLP 0.0008819 0.42661 4.14508
34 2HOX P1T 0.000000002562 0.61892 4.40415
35 4E3Q PMP 0.0003551 0.46887 4.40415
36 3HQP OXL 0.009617 0.41627 4.40415
37 4UHO PLP 0.006737 0.41871 4.66321
38 1B9I PXG 0.0003386 0.40403 4.66321
39 3ZRR PXG 0.00005542 0.45003 4.6875
40 4HVK PMP 0.0001294 0.48165 4.71204
41 5KGS 6SR 0.008623 0.44425 4.92228
42 1F6D UDP 0.007428 0.40726 5.05319
43 4ZM4 PLP 0.0007135 0.44068 5.18135
44 4DW4 U5P 0.005492 0.41818 5.38922
45 1ZC9 PMP 0.004476 0.42875 5.44041
46 3BS8 PMP 0.005104 0.41735 5.44041
47 1WYV PLP AOA 0.001081 0.45633 5.95855
48 5U23 TQP 0.000827 0.48326 6.02094
49 4OKD GLC GLC GLC 0.01005 0.4146 6.21762
50 4AT0 FAD 0.04401 0.40981 6.21762
51 1KJ1 MAN 0.004197 0.42939 6.42202
52 3PNL ADP 0.0178 0.40476 6.63507
53 4BA5 PXG 0.001125 0.42327 6.73575
54 4UOX PLP 0.001991 0.42632 7.51295
55 1DJ9 KAM 0.00022 0.45072 7.55208
56 4RJD TFP 0.01444 0.405 7.57576
57 3IHB GLU 0.02074 0.40066 7.77202
58 4RKC PMP 0.0000001403 0.6354 10.3627
59 1DFO PLG 0.0004561 0.47875 10.3627
60 1E5F PLP 0.00002763 0.49181 10.8911
61 4IY7 KOU 0.0004869 0.42218 11.1399
62 4IYO 0JO 0.0005021 0.42146 11.1399
63 4IY7 0JO 0.0005207 0.42082 11.1399
64 2XBN PMP 0.002747 0.44964 11.399
65 5X2Z 3LM 0.00002373 0.55207 12.1762
66 5X30 7XF 0.00001218 0.48547 12.1762
67 1TOI HCI 0.00471 0.47082 12.1762
68 5X30 4LM 0.0001163 0.45686 12.1762
69 3RYC GDP 0.01297 0.41463 12.1762
70 4K2M O1G 0.000202 0.41635 12.9534
71 1AJS PLA 0.0000005252 0.62927 13.2124
72 2X5F PLP 0.0000001075 0.63288 15.0259
73 1ELU PDA 0.006425 0.42116 15.285
74 1MDZ DCS 0.0003352 0.506 19.9482
75 1MDZ PLP 0.0003142 0.506 19.9482
76 1C7O PPG 0.00001111 0.47219 20.7254
77 1LC8 33P 0.000000008979 0.51495 22.5275
78 4JE5 PMP 0.00000274 0.56734 22.5389
79 4JE5 PLP 0.000002912 0.56611 22.5389
80 3CQ5 PMP 0.00000009716 0.65692 23.3062
81 3PD6 PMP 0.0000001025 0.63386 24.6114
82 3PDB PMP 0.00000006459 0.62583 24.6114
83 1UU1 PMP HSA 0.00000003211 0.55355 28.6567
84 5DJ3 5DK 0.00001184 0.55296 30.8511
85 3B1E P1T 0.000008353 0.52085 31.6062
86 4M2K PLP 0.0000001479 0.63683 33.6788
87 1GEX PLP HSA 0.00000004341 0.50116 34.2697
88 2ZYJ PGU 0.0000006211 0.63288 35.7513
89 3EI9 PL6 0.00000001627 0.54085 36.0104
90 2R2N PMP 0.00000001386 0.65486 36.5285
91 2R2N KYN 0.0000001191 0.45906 36.5285
92 1M7Y PPG 0.00000004862 0.47456 36.7876
93 2ZC0 PMP 0.000000003273 0.62979 39.8964
94 2X5D PLP 0.0000005565 0.55982 41.1917
Pocket No.: 2; Query (leader) PDB : 1U08; Ligand: PLP; 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: 1u08.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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