Receptor
PDB id Resolution Class Description Source Keywords
4ZM4 2.4 Å EC: 2.-.-.- COMPLEX STRUCTURE OF PCTV K276R MUTANT WITH PMP AND 3-DEHYDR STREPTOMYCES PACTUM PYRIDOXAL 5-PHOSPHATE AMINOTRANSFERASE TRANSFERASE
Ref.: MECHANISM-BASED TRAPPING OF THE QUINONOID INTERMEDI USING THE K276R MUTANT OF PLP-DEPENDENT 3-AMINOBENZ SYNTHASE PCTV IN THE BIOSYNTHESIS OF PACTAMYCIN. CHEMBIOCHEM V. 16 2484 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
P3B B:501;
E:501;
Valid;
Valid;
none;
none;
submit data
402.293 C15 H19 N2 O9 P CC1=C...
PLP C:501;
F:501;
A:501;
D:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4ZM4 2.4 Å EC: 2.-.-.- COMPLEX STRUCTURE OF PCTV K276R MUTANT WITH PMP AND 3-DEHYDR STREPTOMYCES PACTUM PYRIDOXAL 5-PHOSPHATE AMINOTRANSFERASE TRANSFERASE
Ref.: MECHANISM-BASED TRAPPING OF THE QUINONOID INTERMEDI USING THE K276R MUTANT OF PLP-DEPENDENT 3-AMINOBENZ SYNTHASE PCTV IN THE BIOSYNTHESIS OF PACTAMYCIN. CHEMBIOCHEM V. 16 2484 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 4ZM3 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4ZM4 - PLP C8 H10 N O6 P Cc1c(c(c(c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 211 families.
1 4ZM3 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4ZM4 - 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 166 families.
1 4ZM3 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4ZM4 - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 2GSA - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
4 3FQ8 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
5 3FQA - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: P3B; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 P3B 1 1
2 PLI 0.530864 0.877193
3 PM9 0.472527 0.769231
4 2B9 0.457447 0.765625
5 P61 0.425743 0.8125
Ligand no: 2; 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 : 4ZM4; Ligand: 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: 4zm4.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found: 82
This union binding pocket(no: 2) in the query (biounit: 4zm4.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IY7 KOU 0.007201 0.41234 1.76322
2 4IY7 0JO 0.008102 0.40997 1.76322
3 4IYO 0JO 0.009768 0.4062 1.76322
4 4Z24 FAD 0.01988 0.41696 2.01342
5 1ZMD FAD 0.03886 0.40301 2.01342
6 1LW4 TLP 0.00005014 0.50955 2.01729
7 1LW4 PLP 0.0000496 0.50452 2.01729
8 4RSL FAD 0.02095 0.4102 2.02247
9 3DR4 G4M 0.000638 0.48738 2.04604
10 2R5C C6P 0.001084 0.45037 2.0979
11 2R5E QLP 0.001466 0.44431 2.0979
12 2R2N PMP 0.00736 0.40789 2.11765
13 5K8B PDG 0.0001036 0.50185 2.23325
14 5X2Z 3LM 0.002621 0.44136 2.26131
15 5X30 7XF 0.001802 0.43815 2.26131
16 5X30 4LM 0.003321 0.42389 2.26131
17 1UU1 PMP HSA 0.01128 0.40668 2.38806
18 1DFO PLG 0.0001972 0.48453 2.39808
19 1AJS PLA 0.005661 0.42237 2.42718
20 2ZC0 PMP 0.00258 0.42891 2.457
21 1PMO PLR 0.001105 0.43567 2.46085
22 2FYF PLP 0.0001554 0.45936 2.51256
23 2VVT I24 0.01674 0.40709 2.75862
24 1GCK ASP PLP 0.003252 0.42832 2.85714
25 1JS3 PLP 142 0.002503 0.40172 2.90828
26 5W71 9YM 0.0006663 0.48875 2.95455
27 5W71 PLP 0.0001366 0.48714 2.95455
28 4E1O PLP PVH 0.006847 0.41685 3.13199
29 4K2M O1G 0.000143 0.43392 3.16027
30 3FRK TQP 0.0008293 0.47276 3.21716
31 5IWQ PLP 0.004318 0.4186 3.22581
32 5DJ3 5DK 0.004887 0.41822 3.45745
33 4WXG 2BO 0.0003718 0.47789 3.73832
34 3VP6 HLD 0.0001777 0.49486 3.80313
35 5W70 9YM 0.0002517 0.47964 3.82022
36 1M32 PLP 0.001638 0.45493 4.09836
37 4LWM MHO 0.03218 0.40272 4.14747
38 1K4M CIT 0.02204 0.40775 4.22535
39 3E2Y PMP 0.0009898 0.43878 4.39024
40 1OXO IK2 0.005637 0.44543 4.48878
41 2PO3 T4K 0.02489 0.40443 4.71698
42 1FC4 AKB PLP 0.001356 0.41541 4.73815
43 2O3Z AI7 0.01828 0.40883 4.79705
44 2F5X ASP 0.01391 0.40766 5.12821
45 1U08 PLP 0.0007135 0.44068 5.18135
46 2ZYJ PGU 0.01389 0.40836 5.28967
47 2WK9 PLG 0.0006328 0.47986 5.39846
48 2WK9 PLP 0.0005699 0.47916 5.39846
49 2HOX P1T 0.006543 0.41239 5.8548
50 1WB4 SXX 0.02097 0.40129 6.06061
51 1SQL GUN 0.02132 0.40096 6.16438
52 3HRD FAD 0.0189 0.41718 8
53 3WGC PLG 0.00009045 0.49269 8.21114
54 1WYV PLP AOA 0.00402 0.4201 8.21918
55 4JSR 1NQ 0.04602 0.40305 8.77193
56 4ZSY RW2 0.000000001417 0.62063 9.61969
57 4AZJ SEP PLP 0.004227 0.42489 10.2778
58 1DJ9 KAM 0.0005258 0.45805 10.4167
59 2X52 GYT 0.01339 0.404 11.1111
60 3WMX THR 0.03347 0.40125 11.1732
61 4CE5 PDG 0.0149 0.40551 11.4114
62 2F5Z FAD 0.04422 0.40014 18.75
63 3PD6 PMP 0.0008566 0.45639 18.9526
64 3PDB PMP 0.0009032 0.43951 18.9526
65 5DDW 5B6 0.000000001459 0.61721 21.7002
66 5KGS 6SR 0.0000000465 0.70046 27.1335
67 3A8U PLP 0.00147 0.48211 27.9642
68 2OAT PFM 0.0000001534 0.5856 29.1572
69 1ZC9 PMP 0.0000003473 0.60867 29.5612
70 4B98 PXG 0.0000000165 0.66586 29.7539
71 4UHO PLP 0.000000007768 0.71965 29.9776
72 2CJH AKG 0.001275 0.47135 30.5122
73 1MLY ACZ PLP 0.00000004725 0.64842 31.4685
74 5G4J EXT 0.00000002071 0.60401 33.1839
75 5WYF ILP 0.00000001051 0.68181 33.557
76 4UOX PLP 0.0000000001923 0.72958 35.123
77 5G09 6DF 0.000000002514 0.71049 35.123
78 4UOX PUT 0.000000005383 0.68418 35.123
79 4UOX PLP PUT 0.00000001716 0.66508 35.123
80 4ADC PLP 0.0000000006094 0.74922 35.468
81 4BA5 PXG 0.0000000277 0.65194 37.3602
82 1SFF IK2 0.0000000004875 0.6553 39.2019
Pocket No.: 3; Query (leader) PDB : 4ZM4; Ligand: P3B; Similar sites found: 52
This union binding pocket(no: 3) in the query (biounit: 4zm4.bio3) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LW4 TLP 0.001062 0.42869 2.01729
2 1LW4 PLP 0.0006936 0.42572 2.01729
3 3DR4 G4M 0.01298 0.40941 2.04604
4 2R5E QLP 0.005132 0.40445 2.0979
5 2R5C C6P 0.006439 0.40027 2.0979
6 5K8B PDG 0.002221 0.42359 2.23325
7 5O4F 8VE 0.02235 0.40057 2.32558
8 1DFO PLG 0.001076 0.43318 2.39808
9 1AJS PLA 0.004994 0.41018 2.42718
10 4C6H HE2 0.02641 0.40102 2.74914
11 1JS3 PLP 142 0.004398 0.40729 2.90828
12 4REP FAD 0.02178 0.40001 2.90828
13 5W71 9YM 0.01762 0.4052 2.95455
14 5W71 PLP 0.003338 0.40319 2.95455
15 4E1O PLP PVH 0.007262 0.40153 3.13199
16 4K2M O1G 0.001192 0.41905 3.16027
17 3FRK TQP 0.009068 0.40874 3.21716
18 4WXG 2BO 0.002145 0.426 3.73832
19 4NV0 MG7 0.01404 0.40259 3.76176
20 3VP6 HLD 0.0005562 0.45305 3.80313
21 5W70 9YM 0.006004 0.40156 3.82022
22 1M32 PLP 0.002998 0.44984 4.09836
23 4LWM MHO 0.01899 0.41492 4.14747
24 4I3G BGC 0.01942 0.40363 4.25056
25 1FC4 AKB PLP 0.005126 0.40788 4.73815
26 2WK9 PLG 0.002824 0.43262 5.39846
27 2WK9 PLP 0.004386 0.42149 5.39846
28 3R9V DXC 0.02904 0.40035 6.99301
29 3WGC PLG 0.001209 0.41606 8.21114
30 4UYG 73B 0.02231 0.40481 8.28025
31 4ZSY RW2 0.00000006405 0.59866 9.61969
32 2GTE VA 0.007634 0.4006 9.67742
33 4AZJ SEP PLP 0.005385 0.40537 10.2778
34 3PD6 PMP 0.00769 0.41924 18.9526
35 5DDW 5B6 0.00000001238 0.62749 21.7002
36 5KGS 6SR 0.0000002468 0.63263 27.1335
37 3A8U PLP 0.007496 0.43181 27.9642
38 2OAT PFM 0.00000007312 0.62532 29.1572
39 1ZC9 PMP 0.000005079 0.5239 29.5612
40 4B98 PXG 0.00000001763 0.61496 29.7539
41 4UHO PLP 0.00000001277 0.72357 29.9776
42 2CJH AKG 0.002079 0.44464 30.5122
43 1MLY ACZ PLP 0.00000002583 0.61862 31.4685
44 5G4J EXT 0.0000005007 0.58109 33.1839
45 5WYF ILP 0.00000004001 0.62048 33.557
46 4UOX PUT 0.00000000164 0.646 35.123
47 4UOX PLP PUT 0.000000008007 0.63048 35.123
48 5G09 6DF 0.00000004975 0.61648 35.123
49 4UOX PLP 0.000000003881 0.60645 35.123
50 4ADC PLP 0.000000003631 0.67429 35.468
51 4BA5 PXG 0.0000009242 0.53491 37.3602
52 1SFF IK2 0.000000003389 0.66581 39.2019
Pocket No.: 4; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found: 11
This union binding pocket(no: 4) in the query (biounit: 4zm4.bio3) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3FV1 DYH 0.02812 0.40057 2.34375
2 2C6Q IMP 0.01825 0.40725 3.1339
3 2C6Q NDP 0.04479 0.40551 3.1339
4 5ECP ATP 0.04393 0.40339 3.3557
5 5ECP MET 0.04605 0.40141 3.3557
6 5ECP JAA 0.04605 0.40141 3.3557
7 4BNU 9KQ 0.003309 0.44068 4.08922
8 5UQW GDP 0.02258 0.40264 4.2328
9 2E5V FAD 0.0372 0.41223 4.47427
10 3PC3 P1T 0.01951 0.4012 4.9217
11 1JG3 ADN 0.01716 0.4005 8.51064
Pocket No.: 5; Query (leader) PDB : 4ZM4; Ligand: P3B; Similar sites found: 5
This union binding pocket(no: 5) in the query (biounit: 4zm4.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1B4N GUA 0.02697 0.40072 1.78971
2 2X41 BGC 0.02659 0.40087 2.46085
3 4BNU 9KQ 0.007846 0.40009 4.08922
4 5U8U FAD 0.04027 0.40383 4.47427
5 2F5Z FAD 0.02285 0.40343 18.75
Pocket No.: 6; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found: 4
This union binding pocket(no: 6) in the query (biounit: 4zm4.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3X0D SAH 0.01888 0.40023 1.78971
2 5X40 ACP 0.01777 0.4048 2.73973
3 3A06 FOM 0.04311 0.40106 2.92553
4 1O94 ADP 0.02422 0.4011 8.75
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