Receptor
PDB id Resolution Class Description Source Keywords
1GDE 1.8 Å EC: 2.6.1.- CRYSTAL STRUCTURE OF PYROCOCCUS PROTEIN A-1 E-FORM PYROCOCCUS HORIKOSHII AMINOTRANSFERASE PYRIDOXAL ENZYME TEMPERATURE DEPENDENCE OSUBSTRATE RECOGNITION TRANSFERASE
Ref.: TEMPERATURE DEPENDENCE OF THE ENZYME-SUBSTRATE RECO MECHANISM. J.BIOCHEM.(TOKYO) V. 129 173 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLU PLP A:414;
A:914;
Valid;
Valid;
none;
none;
submit data
375.25 n/a [P+](...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1GDE 1.8 Å EC: 2.6.1.- CRYSTAL STRUCTURE OF PYROCOCCUS PROTEIN A-1 E-FORM PYROCOCCUS HORIKOSHII AMINOTRANSFERASE PYRIDOXAL ENZYME TEMPERATURE DEPENDENCE OSUBSTRATE RECOGNITION TRANSFERASE
Ref.: TEMPERATURE DEPENDENCE OF THE ENZYME-SUBSTRATE RECO MECHANISM. J.BIOCHEM.(TOKYO) V. 129 173 2001
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1GDE - GLU PLP n/a n/a
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 1GDE - GLU PLP n/a n/a
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: GLU PLP; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 GLU PLP 1 1
2 ASP PLP 0.768116 0.962963
3 SER PLP 0.764706 0.894737
4 PLP MET 0.763889 0.883333
5 MET PLP 0.763889 0.883333
6 LEU PLP 0.757143 0.894737
7 PLP CYS 0.753623 0.894737
8 PLP SEP 0.742857 0.927273
9 SEP PLP 0.742857 0.927273
10 PLP SER 0.720588 0.892857
11 PLP 2TL 0.714286 0.877193
12 PLP TYR 0.710526 0.894737
13 PLP BH2 0.680556 0.877193
14 GLY PLP 0.619718 0.927273
15 PLP 0A0 0.564103 0.896552
16 PLP 2ML 0.5625 0.864407
17 PLP SUO 0.544444 0.870968
18 PLP ALO 0.538462 0.819672
19 CAN PLP 0.505882 0.857143
20 PLP HSA 0.5 0.777778
21 PLP 2KZ 0.47561 0.819672
22 TZA PLP 0.457447 0.83871
23 PLP PMP 0.455696 0.786885
24 PLP ABU 0.425287 0.877193
25 GBC PLP 0.423913 0.806452
26 GAB PLP 0.423913 0.806452
27 PXP 0.405405 0.716667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1GDE; Ligand: GLU PLP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1gde.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1GDE; Ligand: GLU PLP; Similar sites found: 73
This union binding pocket(no: 2) in the query (biounit: 1gde.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TOI HCI 0.0004644 0.5 1.54242
2 2Z9V PXM 0.0008861 0.47443 1.54242
3 1A99 PUT 0.01432 0.41282 1.74419
4 3BWN PMP PHE 0.000000007327 0.66363 2.05656
5 3BWN PMP 0.000000006098 0.61414 2.05656
6 4BG4 ARG 0.02124 0.40737 2.52809
7 5ECP MET 0.0258 0.40029 2.69058
8 2WZF BGC 0.01704 0.41019 3.08483
9 1CL2 PPG 0.003547 0.40738 3.3419
10 2HOX P1T 0.000000001058 0.69292 3.59897
11 3WMX THR 0.01186 0.40964 3.63128
12 2FYF PLP 0.01284 0.41084 4.62725
13 5GVL GI8 0.009515 0.41975 4.88432
14 5GVL PLG 0.009515 0.41975 4.88432
15 4IYO 0JO 0.0004684 0.4528 5.9126
16 4IY7 KOU 0.0004206 0.44587 5.9126
17 4IY7 0JO 0.0004457 0.44476 5.9126
18 5X30 7XF 0.0002023 0.46626 6.16967
19 5X2Z 3LM 0.0006819 0.45515 6.16967
20 5X30 4LM 0.001017 0.43191 6.16967
21 4AZJ SEP PLP 0.001347 0.41994 6.38889
22 2XBN PMP 0.007998 0.40765 6.94087
23 2TPL HPP 0.001046 0.40189 7.19794
24 1E5F PLP 0.000216 0.47504 7.45501
25 1YAA MAE 0.00008476 0.4273 8.99743
26 3ZRR PXG 0.001848 0.41958 9.375
27 2AY3 MPP 0.000009903 0.54189 9.51157
28 5DJ3 5DK 0.0001085 0.47787 10.3723
29 5LE1 6UW 0.02552 0.40082 10.5263
30 3WGC PLG 0.002945 0.40801 10.5572
31 2WK9 PLG 0.001414 0.44995 11.054
32 2WK9 PLP 0.001517 0.44581 11.054
33 5W70 9YM 0.003272 0.41631 12.5843
34 1F6D UDP 0.01484 0.40357 12.766
35 5K8B PDG 0.00625 0.40766 12.8535
36 1DJ9 KAM 0.002414 0.42801 13.5417
37 3FRK TQP 0.005812 0.42071 13.6729
38 4RKC PMP 0.000000936 0.54498 14.3959
39 5U23 TQP 0.006374 0.41889 14.3979
40 2OGA PGU 0.002994 0.41986 14.653
41 2FNU PMP UD1 0.01012 0.41543 16.5333
42 1OXO IK2 0.000001904 0.41509 16.7095
43 1LW4 TLP 0.002578 0.41881 16.7147
44 1LW4 PLP 0.001816 0.41636 16.7147
45 1MDZ PLP 0.01433 0.40404 16.9666
46 1MDZ DCS 0.01517 0.40404 16.9666
47 2CST MAE 0.001111 0.46943 21.0797
48 1AJS PLA 0.0000000215 0.64931 22.365
49 1FC4 AKB PLP 0.002929 0.41643 22.365
50 2X5F PLP 0.000000006855 0.70892 22.6221
51 3PDB PMP 0.0000005077 0.60971 22.6221
52 3PD6 PMP 0.00000113 0.60212 22.6221
53 3PD6 KYN 0.00002133 0.56078 22.6221
54 3PDB OAA 0.0006789 0.47331 22.6221
55 5IWQ PLP 0.000004499 0.56518 25.4499
56 1UU1 PMP HSA 0.00000008094 0.58675 27.7612
57 1GEX PLP HSA 0.0000003932 0.51817 28.0899
58 1LC8 33P 0.0000006199 0.50244 28.8462
59 3CQ5 PMP 0.00000001498 0.5586 31.9783
60 4M2K PLP 0.0000005439 0.51705 34.4473
61 4JE5 PMP 0.0000005703 0.61642 36.7609
62 4JE5 PLP 0.0000007211 0.61151 36.7609
63 1M7Y PPG 0.0000003905 0.60791 38.5604
64 3EI9 PL6 0.000000002851 0.61871 40.1028
65 3B1E P1T 0.0000002174 0.5675 43.7018
66 2ZYJ PGU 0.000000000134 0.75575 45.5919
67 2R2N PMP 0.000000002521 0.718 46.7866
68 3E2Y PMP 0.000000002149 0.62696 46.7866
69 1C7O PPG 0.0000002925 0.57562 46.7866
70 2R2N KYN 0.000194 0.51631 46.7866
71 2X5D PLP 0.00000003318 0.53459 48.329
72 2ZC0 PMP 0.00000006479 0.62443 48.5861
73 3FVU IAC 0.00002552 0.42847 49.1003
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