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 307 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 275 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 (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 212 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 3FQA - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: P3B; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 P3B 1 1
2 PLI 0.530864 0.877193
3 LJS 0.488889 0.912281
4 PM9 0.472527 0.769231
5 2B9 0.457447 0.765625
6 P71 0.457447 0.87931
7 EMS 0.443299 0.806452
8 EJ1 0.438776 0.784615
9 P61 0.425743 0.8125
Ligand no: 2; Ligand: PLP; Similar ligands found: 62
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 F0G 0.564516 0.865385
13 FEV 0.555556 0.803571
14 KOU 0.555556 0.836364
15 EVM 0.546875 0.821429
16 HCP 0.546875 0.77193
17 6DF 0.545455 0.811321
18 PXL 0.541667 0.659574
19 Z98 0.537313 0.75
20 PXP 0.537037 0.862745
21 P0P 0.527273 0.916667
22 PMP 0.527273 0.767857
23 PL6 0.522388 0.818182
24 GT1 0.517857 0.830189
25 FEJ 0.514706 0.851852
26 PFM 0.514706 0.803571
27 LLP 0.5 0.737705
28 P70 0.5 0.833333
29 PL5 0.479452 0.775862
30 PUS 0.479452 0.707692
31 MPL 0.473684 0.836364
32 IN5 0.46875 0.758621
33 PLG 0.46875 0.75
34 P89 0.466667 0.714286
35 PLP PUT 0.463768 0.672131
36 5DK 0.460526 0.725806
37 EQJ 0.460526 0.725806
38 O1G 0.454545 0.75
39 PLT 0.439024 0.762712
40 X04 0.431034 0.851852
41 PDA 0.426471 0.762712
42 PDD 0.426471 0.762712
43 P1T 0.426471 0.714286
44 PP3 0.426471 0.762712
45 IK2 0.42029 0.714286
46 CKT 0.42029 0.762712
47 33P 0.42029 0.745763
48 2BK 0.414286 0.793103
49 PLS 0.414286 0.779661
50 2BO 0.414286 0.793103
51 5PA 0.414286 0.714286
52 TLP 0.414286 0.793103
53 PMH 0.414286 0.619718
54 9TD 0.413793 0.671642
55 PLP 999 0.410959 0.796296
56 PPD 0.408451 0.75
57 C6P 0.408451 0.75
58 QLP 0.405405 0.681818
59 MP5 0.403509 0.666667
60 PY5 0.402778 0.703125
61 PLA 0.402778 0.703125
62 HEY 0.4 0.703125
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found with APoc: 32
This union binding pocket(no: 1) in the query (biounit: 4zm4.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZSY RW2 9.61969
2 4ZSY RW2 9.61969
3 5DDW 5B6 21.7002
4 5DDW 5B6 21.7002
5 5DDW 5B6 21.7002
6 5DDW 5B6 21.7002
7 5KGS 6SR 27.1335
8 5KGS 6SR 27.1335
9 4B98 PXG 29.7539
10 4B98 PXG 29.7539
11 4B98 PXG 29.7539
12 4B98 PXG 29.7539
13 1MLY ACZ PLP 31.4685
14 5WYF ILP 33.557
15 5WYF ILP 33.557
16 5WYF ILP 33.557
17 4UOX PLP 35.123
18 5G09 6DF 35.123
19 5G09 6DF 35.123
20 5G09 6DF 35.123
21 5G09 6DF 35.123
22 4UOX PLP 35.123
23 4ADC PLP 35.468
24 4ADC PLP 35.468
25 6S4G PMP 37.3602
26 6S4G PMP 37.3602
27 6S4G PMP 37.3602
28 6S4G PMP 37.3602
29 1SFF IK2 39.2019
30 1SFF IK2 39.2019
31 1SFF IK2 39.2019
32 1SFF IK2 39.2019
Pocket No.: 2; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found with APoc: 23
This union binding pocket(no: 2) in the query (biounit: 4zm4.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZSY RW2 9.61969
2 4ZSY RW2 9.61969
3 5DDW 5B6 21.7002
4 5DDW 5B6 21.7002
5 5DDW 5B6 21.7002
6 5DDW 5B6 21.7002
7 5KGS 6SR 27.1335
8 5KGS 6SR 27.1335
9 4UOX PLP 35.123
10 4UOX PLP 35.123
11 5G09 6DF 35.123
12 5G09 6DF 35.123
13 5G09 6DF 35.123
14 5G09 6DF 35.123
15 4ADC PLP 35.468
16 4ADC PLP 35.468
17 6S4G PMP 37.3602
18 6S4G PMP 37.3602
19 6S4G PMP 37.3602
20 1SFF IK2 39.2019
21 1SFF IK2 39.2019
22 1SFF IK2 39.2019
23 1SFF IK2 39.2019
Pocket No.: 3; Query (leader) PDB : 4ZM4; Ligand: P3B; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 4zm4.bio3) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 3A8U PLP 27.9642
2 3A8U PLP 27.9642
3 4UHO PLP 29.9776
4 4UOX PLP 35.123
5 4UOX PLP 35.123
6 4UOX PUT 35.123
7 4ADC PLP 35.468
8 4ADC PLP 35.468
Pocket No.: 4; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found with APoc: 17
This union binding pocket(no: 4) in the query (biounit: 4zm4.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5DDW 5B6 21.7002
2 5DDW 5B6 21.7002
3 5DDW 5B6 21.7002
4 5DDW 5B6 21.7002
5 3A8U PLP 27.9642
6 3A8U PLP 27.9642
7 4B98 PXG 29.7539
8 4B98 PXG 29.7539
9 4B98 PXG 29.7539
10 4B98 PXG 29.7539
11 4UHO PLP 29.9776
12 4UOX PLP 35.123
13 4UOX PLP 35.123
14 4ADC PLP 35.468
15 4ADC PLP 35.468
16 6S4G PMP 37.3602
17 6S4G PMP 37.3602
Pocket No.: 5; Query (leader) PDB : 4ZM4; Ligand: P3B; Similar sites found with APoc: 10
This union binding pocket(no: 5) in the query (biounit: 4zm4.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 3A8U PLP 27.9642
2 3A8U PLP 27.9642
3 4UHO PLP 29.9776
4 4UOX PLP 35.123
5 4UOX PLP 35.123
6 4UOX PUT 35.123
7 4ADC PLP 35.468
8 4ADC PLP 35.468
9 6S4G PMP 37.3602
10 6S4G PMP 37.3602
Pocket No.: 6; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found with APoc: 11
This union binding pocket(no: 6) in the query (biounit: 4zm4.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5DDW 5B6 21.7002
2 5DDW 5B6 21.7002
3 3A8U PLP 27.9642
4 3A8U PLP 27.9642
5 4UHO PLP 29.9776
6 4UOX PLP 35.123
7 4UOX PLP 35.123
8 4ADC PLP 35.468
9 4ADC PLP 35.468
10 6S4G PMP 37.3602
11 6S4G PMP 37.3602
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