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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
6C9B 1.69 Å EC: 3.-.-.- THE STRUCTURE OF MPPP SOAKED WITH THE PRODUCTS 4HKA AND 2KA STREPTOMYCES WADAYAMENSIS DIMER PRODUCT 4HKA BINDING COMPLEX OXIDASE PLP ANTIBIOTIOXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX
Ref.: STREPTOMYCES WADAYAMENSIS MPPP IS A PLP-DEPENDENT O NOT AN OXYGENASE. BIOCHEMISTRY V. 57 3252 2018
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 5BK7 - EQJ C14 H22 N5 O7 P [H]/N=C(/N....
2 6C9B - EGV C6 H11 N3 O4 [H]/N=C(/N....
3 5DJ3 - 5DK C14 H22 N5 O7 P [H]/N=C(N)....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 5BK7 - EQJ C14 H22 N5 O7 P [H]/N=C(/N....
2 6C9B - EGV C6 H11 N3 O4 [H]/N=C(/N....
3 5DJ3 - 5DK C14 H22 N5 O7 P [H]/N=C(N)....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 173 families.
1 5BK7 - EQJ C14 H22 N5 O7 P [H]/N=C(/N....
2 6C9B - EGV C6 H11 N3 O4 [H]/N=C(/N....
3 5DJ3 - 5DK C14 H22 N5 O7 P [H]/N=C(N)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5DK; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 5DK 1 1
2 EQJ 1 1
3 PL5 0.7125 0.903226
4 PL6 0.679487 0.854839
5 KOU 0.671053 0.84127
6 PUS 0.630952 0.8
7 F0G 0.615385 0.806452
8 P70 0.593023 0.809524
9 EPC 0.584416 0.774194
10 FEJ 0.571429 0.769231
11 0JO 0.5625 0.784615
12 Z98 0.552941 0.904762
13 LLP 0.539326 0.920635
14 PLT 0.53125 0.776119
15 4LM 0.52439 0.769231
16 6DF 0.523256 0.734375
17 FEV 0.511905 0.757576
18 MET PLP 0.511111 0.720588
19 EVM 0.505882 0.828125
20 P3D 0.488372 0.888889
21 PLP PHE 0.484211 0.75
22 PFM 0.483146 0.8125
23 MPM 0.482353 0.765625
24 EXT 0.481928 0.83871
25 FOO 0.481928 0.793651
26 AN7 0.46988 0.730159
27 PLP 999 0.466667 0.75
28 PLP PVH 0.464646 0.732394
29 P89 0.463158 0.757143
30 PLP 0.460526 0.725806
31 HCP 0.454545 0.784615
32 PZP 0.454545 0.758065
33 PL2 0.445652 0.878788
34 3QP 0.426966 0.758065
35 O1G 0.424242 0.714286
36 KET 0.423913 0.828125
37 PLP MYB 0.415842 0.689189
38 PLP PUT 0.413043 0.857143
39 PLS 0.406593 0.818182
40 ORX 0.40625 0.863636
41 C6P 0.402174 0.818182
42 PE1 0.402062 0.863636
43 QLP 0.4 0.8
44 LPI 0.4 0.763889
45 PDA 0.4 0.776119
46 PDD 0.4 0.776119
47 PP3 0.4 0.776119
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6C9B; Ligand: EGV; Similar sites found with APoc: 138
This union binding pocket(no: 1) in the query (biounit: 6c9b.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 2OGA PGU 1.59574
2 4UOX PUT 1.8617
3 4UOX PLP 1.8617
4 2HOX P1T 2.12766
5 5GVL GI8 2.12766
6 5GVL PLG 2.12766
7 2FYF PLP 2.12766
8 4E3Q PMP 2.39362
9 5A2Z GTP 2.39362
10 1ELU CSS 2.39362
11 1WD4 AHR 2.39362
12 1ELU PDA 2.39362
13 6CZY PMP 2.48619
14 1DKU ABM 2.52366
15 4YGF AZM 2.5641
16 4OIT MAN 2.65487
17 2JAP J01 2.83401
18 4ZM4 PLP 2.92553
19 4LNL PLG 3.003
20 4LNL 2BK 3.003
21 4LNL 2BO 3.003
22 6ECG PM9 3.19149
23 1JS3 PLP 142 3.19149
24 4UHO PLP 3.19149
25 2TPL HPP 3.19149
26 3WYW GSH 3.24074
27 1LT3 GAL BGC 3.33333
28 1JLV GSH 3.34928
29 4YGM URA 3.44828
30 5W71 PLP 3.45745
31 1PMO PLR 3.45745
32 3ZRR PXG 3.45745
33 4GC1 MAN MAN 3.62319
34 4URS C2E 3.7234
35 2V7B BEZ 3.7234
36 6EWR PMP 3.98936
37 5W70 9YM 3.98936
38 6D50 GCB 3.98936
39 5Z2F PDC 4.15094
40 4HVK PMP 4.18848
41 1CL2 PPG 4.25532
42 2PO3 T4K 4.25532
43 3E81 SLB 4.26829
44 2Z9V PXM 4.52128
45 5K8B PDG 4.52128
46 5LXB 7A9 4.54545
47 4A7W GTP 4.58333
48 2R2N PMP 4.78723
49 1FC4 AKB PLP 4.78723
50 2R2N KYN 4.78723
51 5GMH RX8 4.78723
52 5X30 7XF 5.05319
53 4WXG 2BO 5.05319
54 5X30 4LM 5.05319
55 5X2Z 3LM 5.05319
56 5GWE GWM 5.05319
57 4JE5 PMP 5.31915
58 4JE5 PLP 5.31915
59 2AY3 MPP 5.31915
60 1WYV PLP AOA 5.31915
61 3CEV ARG 5.35117
62 3M0J OAF 5.53746
63 5NN6 MIG 5.58511
64 4RKC PMP 5.85106
65 3A8U PLP 5.85106
66 5WYF ILP 5.85106
67 3KP6 SAL 5.96026
68 1E5F PLP 6.11702
69 6CD1 PLS 6.11702
70 6CD1 PLG 6.11702
71 4K2M O1G 6.11702
72 1LW4 PLP 6.34006
73 1LW4 TLP 6.34006
74 2CST MAE 6.38298
75 3U6W KIV 6.38298
76 2Y6P CTP 6.41026
77 3WGC PLG 6.45161
78 5UMW RBF 6.62252
79 5YKT PMP 6.64894
80 4B98 PXG 6.64894
81 4BA5 PXG 6.91489
82 1LTT GAL BGC 7.02703
83 1DFO PLG 7.18085
84 5M3Z PY6 7.44681
85 5M3Z PLP 7.44681
86 4RJD TFP 7.57576
87 6DND PLP 7.71277
88 1AJS PLA 7.71277
89 1UU1 PMP HSA 7.76119
90 2CHT TSA 7.87402
91 2X5D PLP 7.97872
92 1XI9 PLP 7.97872
93 4IY7 KOU 8.24468
94 4IY7 0JO 8.24468
95 4IYO 0JO 8.24468
96 1DJ9 KAM 8.51064
97 5T85 44G 8.58896
98 2X5F PLP 8.7766
99 4GDX GLU 8.82353
100 3BWN PMP PHE 9.04255
101 3BWN PMP 9.04255
102 5IWQ PLP 9.04255
103 5TXR PLP 9.30851
104 5W19 9TD 9.30851
105 4FL0 PLP 9.84043
106 1C7O PPG 10.1064
107 5N1X 8HH 10.1695
108 2R5E QLP 10.3723
109 2R5C C6P 10.3723
110 1GDE GLU PLP 10.3723
111 4E1O PLP PVH 10.3723
112 4LZB URA 10.5042
113 3FVU IAC 11.1702
114 1R87 XYP XYP 11.4362
115 5VEQ PMP 11.7021
116 3CQ5 PMP 12.1951
117 1YAA MAE 12.234
118 3K8D CTP 12.5
119 4R5Z PMP 12.5341
120 4R5Z SIN 12.5341
121 1GCK ASP PLP 13.5638
122 3VP6 HLD 13.8298
123 1OXO IK2 13.8298
124 3EI9 PL6 14.3617
125 5T4J PLP ABU 14.5205
126 1TOI HCI 14.6277
127 2ZC0 PMP 15.1596
128 3PDB PMP 15.4255
129 2ZYJ PGU 15.4255
130 3PD6 PMP 15.4255
131 1KJ1 MAN 15.5963
132 4M2K PLP 16.2234
133 1LC8 33P 16.7582
134 1GEX PLP HSA 16.8539
135 1M7Y PPG 17.0213
136 1V2F HCI 18.3511
137 2YJP CYS 25.7732
138 1U08 PLP 30.5851
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