Receptor
PDB id Resolution Class Description Source Keywords
5DJ3 2.23 Å EC: 3.-.-.- STRUCTURE OF THE PLP-DEPENDENT L-ARGININE HYDROXYLASE MPPP W ARGININE BOUND STREPTOMYCES WADAYAMENSIS AMINOTRANSFERASE HYDROXYLASE ENDURACIDIDINE PYRIDOXAL 5-prime -PHOSPHATE TRANSFERASE
Ref.: STREPTOMYCES WADAYAMENSIS MPPP IS A PYRIDOXAL 5'-PHOSPHATE-DEPENDENT L-ARGININE ALPHA-DEAMINASE, GAMMA-HYDROXYLASE IN THE ENDURACIDIDINE BIOSYNTHETI PATHWAY. BIOCHEMISTRY V. 54 7029 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5DK B:401;
C:500;
A:500;
D:500;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
403.328 C14 H22 N5 O7 P [H]/N...
MG B:402;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DJ3 2.23 Å EC: 3.-.-.- STRUCTURE OF THE PLP-DEPENDENT L-ARGININE HYDROXYLASE MPPP W ARGININE BOUND STREPTOMYCES WADAYAMENSIS AMINOTRANSFERASE HYDROXYLASE ENDURACIDIDINE PYRIDOXAL 5-prime -PHOSPHATE TRANSFERASE
Ref.: STREPTOMYCES WADAYAMENSIS MPPP IS A PYRIDOXAL 5'-PHOSPHATE-DEPENDENT L-ARGININE ALPHA-DEAMINASE, GAMMA-HYDROXYLASE IN THE ENDURACIDIDINE BIOSYNTHETI PATHWAY. BIOCHEMISTRY V. 54 7029 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 5DJ3 - 5DK C14 H22 N5 O7 P [H]/N=C(N)....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 176 families.
1 5DJ3 - 5DK C14 H22 N5 O7 P [H]/N=C(N)....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 143 families.
1 5DJ3 - 5DK C14 H22 N5 O7 P [H]/N=C(N)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5DK; Similar ligands found: 39
No: Ligand ECFP6 Tc MDL keys Tc
1 5DK 1 1
2 PL5 0.7125 0.903226
3 PL6 0.679487 0.854839
4 KOU 0.671053 0.84127
5 PUS 0.630952 0.8
6 EPC 0.584416 0.774194
7 0JO 0.5625 0.784615
8 Z98 0.552941 0.904762
9 LLP 0.539326 0.920635
10 PLT 0.53125 0.776119
11 4LM 0.52439 0.769231
12 6DF 0.523256 0.734375
13 P3D 0.488372 0.888889
14 PLP PHE 0.484211 0.75
15 PFM 0.483146 0.8125
16 MPM 0.482353 0.765625
17 EXT 0.481928 0.83871
18 FOO 0.481928 0.793651
19 AN7 0.46988 0.730159
20 PLP PVH 0.464646 0.732394
21 P89 0.463158 0.757143
22 PLP 0.460526 0.725806
23 HCP 0.454545 0.784615
24 PZP 0.454545 0.758065
25 PL2 0.445652 0.878788
26 PLP ABU 0.434783 0.809524
27 PLP PUT 0.428571 0.761905
28 3QP 0.426966 0.758065
29 O1G 0.424242 0.714286
30 KET 0.423913 0.828125
31 PLP MYB 0.415842 0.689189
32 PLS 0.406593 0.818182
33 ORX 0.40625 0.863636
34 C6P 0.402174 0.818182
35 PE1 0.402062 0.863636
36 QLP 0.4 0.8
37 PP3 0.4 0.776119
38 PDA 0.4 0.776119
39 PDD 0.4 0.776119
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DJ3; Ligand: 5DK; Similar sites found: 75
This union binding pocket(no: 1) in the query (biounit: 5dj3.bio3) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WK9 PLG 0.001345 0.45093 1.06383
2 2WK9 PLP 0.004069 0.42644 1.06383
3 2OGA PGU 0.002284 0.42497 1.59574
4 4UOX PUT 0.007738 0.40526 1.8617
5 2HOX P1T 0.000000685 0.57228 2.12766
6 2FYF PLP 0.003955 0.43621 2.12766
7 5GVL GI8 0.005536 0.43075 2.12766
8 5GVL PLG 0.005536 0.43075 2.12766
9 4E3Q PMP 0.0006964 0.46771 2.39362
10 1ELU PDA 0.002471 0.4196 2.39362
11 3SZB I1E 0.01529 0.41481 2.92553
12 1JS3 PLP 142 0.001407 0.43011 3.19149
13 4UHO PLP 0.009618 0.42177 3.19149
14 1PMO PLR 0.003551 0.42897 3.45745
15 5W71 9YM 0.007807 0.42475 3.45745
16 5W71 PLP 0.0015 0.42396 3.45745
17 4ZM4 PLP 0.004887 0.41822 3.45745
18 5W70 9YM 0.002024 0.41682 3.7234
19 3EFS ATP 0.009312 0.41337 3.86266
20 5K8B PDG 0.002218 0.40468 4.52128
21 1MAI I3P 0.02241 0.41212 4.58015
22 2R2N PMP 0.0001086 0.50019 4.78723
23 1FC4 AKB PLP 0.0002111 0.46547 4.78723
24 5X2Z 3LM 0.0005555 0.45911 5.05319
25 4WXG 2BO 0.00009172 0.44976 5.05319
26 5X30 7XF 0.0005244 0.44851 5.05319
27 5X30 4LM 0.001504 0.43295 5.05319
28 4JE5 PMP 0.0002635 0.48805 5.31915
29 4JE5 PLP 0.0002697 0.48756 5.31915
30 2AY3 MPP 0.007183 0.41053 5.31915
31 1WYV PLP AOA 0.009667 0.40091 5.31915
32 4RKC PMP 0.0001546 0.48711 5.85106
33 1LW4 TLP 0.000136 0.47366 6.34006
34 1LW4 PLP 0.00007358 0.4728 6.34006
35 5U23 TQP 0.008888 0.41232 6.38298
36 3WGC PLG 0.00006656 0.49797 6.45161
37 4B98 PXG 0.004002 0.40599 6.64894
38 4BA5 PXG 0.00997 0.4003 6.91489
39 1DFO PLG 0.001577 0.43001 7.18085
40 1AJS PLA 0.00001684 0.52222 7.71277
41 1XI9 PLP 0.00001438 0.55682 7.97872
42 2X5D PLP 0.00006277 0.5352 7.97872
43 4IY7 KOU 0.0002388 0.45684 8.24468
44 4IYO 0JO 0.0002677 0.45489 8.24468
45 4IY7 0JO 0.0002795 0.45414 8.24468
46 1DJ9 KAM 0.0004684 0.45996 8.51064
47 2X5F PLP 0.00006662 0.51682 8.7766
48 5CQG 55C 0.01603 0.4124 8.7766
49 4GDX GLU 0.01378 0.41652 8.82353
50 3BWN PMP 0.00002507 0.53012 9.04255
51 3BWN PMP PHE 0.000009163 0.50564 9.04255
52 5IWQ PLP 0.0001004 0.5018 9.04255
53 1ZC9 PMP 0.003633 0.41241 9.30851
54 1UU1 PMP HSA 0.00007674 0.46849 9.84043
55 1C7O PPG 0.000008698 0.51441 10.1064
56 2R5C C6P 0.000002451 0.55131 10.3723
57 2R5E QLP 0.000002373 0.53807 10.3723
58 1GDE GLU PLP 0.0001085 0.47787 10.3723
59 2RC8 DSN 0.02057 0.40287 11.9048
60 3CQ5 PMP 0.000002732 0.60189 12.1951
61 4R5Z PMP 0.0001367 0.4514 12.8065
62 4R5Z SIN 0.0001357 0.42468 12.8065
63 1GCK ASP PLP 0.0000716 0.4775 13.2979
64 3B1E P1T 0.000000859 0.59061 13.8298
65 3VP6 HLD 0.0004379 0.46191 13.8298
66 3EI9 PL6 0.00000849 0.4918 14.3617
67 3E2Y PMP 0.00005194 0.51525 14.6277
68 2ZC0 PMP 0.0002445 0.46756 15.1596
69 3PDB PMP 0.00007862 0.50678 15.4255
70 3PD6 PMP 0.000113 0.50577 15.4255
71 2ZYJ PGU 0.000008814 0.46744 15.4255
72 1V2F HCI 0.008376 0.42006 18.3511
73 4JGT PYR 0.01606 0.40633 19.398
74 4FL0 PLP 0.00005726 0.51326 26.8617
75 1U08 PLP 0.00001184 0.55296 30.8511
Pocket No.: 2; Query (leader) PDB : 5DJ3; Ligand: 5DK; 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: 5dj3.bio3) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5DJ3; Ligand: 5DK; 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: 5dj3.bio3) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5DJ3; Ligand: 5DK; 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: 5dj3.bio3) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5DJ3; Ligand: 5DK; Similar sites found: 3
This union binding pocket(no: 5) in the query (biounit: 5dj3.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2FAH MLA 0.01086 0.41343 1.8617
2 4X5S AZM 0.01873 0.40753 3.44828
3 3PDB OAA 0.02665 0.40607 15.4255
Pocket No.: 6; Query (leader) PDB : 5DJ3; Ligand: 5DK; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5dj3.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5DJ3; Ligand: 5DK; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5dj3.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5DJ3; Ligand: 5DK; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5dj3.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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