Receptor
PDB id Resolution Class Description Source Keywords
4B9B 1.64 Å EC: 2.6.1.18 THE STRUCTURE OF THE OMEGA AMINOTRANSFERASE FROM PSEUDOMONAS AERUGINOSA PSEUDOMONAS AERUGINOSA TRANSFERASE
Ref.: STRUCTURAL STUDIES WITH PSEUDOMONAS AND CHROMOBACTE [OMEGA]-AMINOTRANSFERASES PROVIDE INSIGHTS INTO THE DIFFERING SUBSTRATE SPECIFICITY. ACTA CRYSTALLOGR.,SECT.D V. 69 564 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLP F:500;
D:500;
C:500;
A:500;
G:500;
E:500;
H:500;
B:500;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
CL E:502;
D:502;
F:502;
G:502;
C:502;
B:502;
H:502;
A:502;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
CA F:503;
E:503;
G:503;
H:503;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
GOL A:501;
G:504;
H:504;
H:501;
B:504;
E:504;
C:504;
F:501;
C:501;
A:504;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4B98 1.65 Å EC: 2.6.1.18 THE STRUCTURE OF THE OMEGA AMINOTRANSFERASE FROM PSEUDOMONAS AERUGINOSA PSEUDOMONAS AERUGINOSA TRANSFERASE
Ref.: STRUCTURAL STUDIES WITH PSEUDOMONAS AND CHROMOBACTE [OMEGA]-AMINOTRANSFERASES PROVIDE INSIGHTS INTO THE DIFFERING SUBSTRATE SPECIFICITY. ACTA CRYSTALLOGR.,SECT.D V. 69 564 2013
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4BQ0 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4B9B - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 4B98 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4UHM - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4UHN - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 4UHO - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 4BQ0 - PLP C8 H10 N O6 P Cc1c(c(c(c....
5 4B9B - PLP C8 H10 N O6 P Cc1c(c(c(c....
6 4B98 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
7 3A8U - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
2 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
3 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
4 4MQR - 2B9 C14 H15 N4 O6 P CC1=C(/C(=....
5 4MQP - 2B1 C15 H15 N4 O5 P S Cc1c(c(c(c....
6 4XJO Kd = 132 nM 41O C20 H17 Cl N2 O2 c1cc(cc(c1....
7 5KGS Kd = 74 nM 6SR C21 H20 N2 O4 c1cc2c(cc1....
8 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
9 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
10 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
11 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
12 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
13 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
14 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
15 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
16 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
17 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
18 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
19 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
20 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
21 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
22 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
23 4B9B - PLP C8 H10 N O6 P Cc1c(c(c(c....
24 4B98 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
25 1MLZ - TZA PLP n/a n/a
26 1MLY - ACZ PLP n/a n/a
27 1S07 - PLP C8 H10 N O6 P Cc1c(c(c(c....
28 3DU4 - KAP C9 H17 N O3 C[C@@H](C(....
29 3A8U - 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 : 4B98; Ligand: PXG; Similar sites found: 68
This union binding pocket(no: 1) in the query (biounit: 4b98.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4K2M O1G 0.001347 0.40898 1.3544
2 1XI9 PLP 0.0141 0.40694 1.72414
3 2FYF PLP 0.00007743 0.51817 1.75879
4 3PD6 PMP 0.003671 0.43087 1.99501
5 3PDB PMP 0.007384 0.41204 1.99501
6 2WZF BGC 0.01416 0.41331 2.00893
7 5U23 TQP 0.005521 0.42527 2.09424
8 4E1O PLP PVH 0.001024 0.41332 2.23214
9 5GVL GI8 0.001893 0.45651 2.48869
10 5GVL PLG 0.001893 0.45651 2.48869
11 5X2Z 3LM 0.000754 0.45758 2.51256
12 5X30 7XF 0.002694 0.41403 2.51256
13 5X30 4LM 0.004483 0.4101 2.51256
14 2OGA PGU 0.008719 0.403 2.75689
15 1B9I PXG 0.006678 0.41151 2.83505
16 5W71 9YM 0.009492 0.42409 2.95455
17 5W71 PLP 0.003675 0.41387 2.95455
18 4LNL PLG 0.001322 0.42273 3.003
19 4LNL 2BO 0.001808 0.42224 3.003
20 3VP6 HLD 0.001099 0.44848 3.125
21 1DMH MCT 0.01761 0.40216 3.21543
22 1VJO PLP 0.001497 0.43517 3.30789
23 1JS3 PLP 142 0.004244 0.40529 3.34821
24 4IY7 0JO 0.003918 0.40218 3.77834
25 4IY7 KOU 0.004082 0.40171 3.77834
26 3ZRR PXG 0.0000283 0.487 3.90625
27 5W3Y ACO 0.02125 0.40099 3.97727
28 2X5F PLP 0.01136 0.40729 4.4186
29 1PMO PLR 0.003996 0.42453 4.46429
30 4JUI EGR 0.01705 0.40878 4.46429
31 2Z9V PXM 0.002097 0.45332 4.59184
32 1LW4 PLP 0.0002426 0.45864 4.61095
33 1LW4 TLP 0.0004371 0.45649 4.61095
34 3WGC PLG 0.001294 0.42843 4.69208
35 4M2K PLP 0.008735 0.41722 4.92611
36 1M32 PLP 0.0008158 0.47469 5.7377
37 5DJ3 5DK 0.004002 0.40599 6.64894
38 1ELU PDA 0.0004328 0.44747 6.66667
39 1ELU CSS 0.0005929 0.42859 6.66667
40 3HQ9 OXL 0.01109 0.41512 6.66667
41 2IZ1 ATR 0.01822 0.40742 6.69643
42 2XRH NIO 0.002707 0.44513 7
43 1DFO PLG 0.001296 0.43784 7.19424
44 4F8L AES 0.01345 0.41446 7.58621
45 2YP6 C6W 0.004968 0.42768 8.64865
46 4AZJ SEP PLP 0.0001201 0.45678 9.72222
47 1FC4 AKB PLP 0.000159 0.46564 9.97506
48 2CJH AKG 0.0000001649 0.6116 20.7589
49 5DDW 5B6 0.00000002957 0.59235 22.7679
50 4ZSY RW2 0.000000003915 0.62706 24.7768
51 1DJ9 KAM 0.004136 0.41548 29.6875
52 4ZM4 PLP 0.0000000165 0.66586 29.7539
53 4ZM4 P3B 0.00000001763 0.61496 29.7539
54 2YKX AKG 0.0007601 0.48258 31.4732
55 4AOA IK2 0.00000000886 0.66819 32.5893
56 4UOX PLP 0.000000000871 0.7358 33.9286
57 4UOX PUT 0.000000002276 0.69449 33.9286
58 4UOX PLP PUT 0.000000007503 0.66186 33.9286
59 3FQ8 PMP 0.000000009931 0.67301 37.0023
60 3BS8 PMP 0.00000003724 0.59412 37.2768
61 1SFF IK2 0.000000004298 0.63917 38.7324
62 5G4J EXT 0.000002039 0.54398 39.6861
63 4E3Q PMP 0.0000000003215 0.76892 43.5268
64 1ZC9 PMP 0.00000002257 0.64452 43.8799
65 5WYF ILP 0.000000004388 0.64024 44.6429
66 4ADC PLP 0.000000009077 0.5854 44.8276
67 2OAT PFM 0.00000003791 0.6312 44.8747
68 5G09 6DF 0.000000001471 0.65976 47.0982
Pocket No.: 2; Query (leader) PDB : 4B98; Ligand: PXG; 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: 4b98.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4B98; Ligand: PXG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4b98.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4B98; Ligand: PXG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4b98.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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