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Receptor
PDB id Resolution Class Description Source Keywords
2WBO 1.3 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF VIOC IN COMPLEX WITH L-ARGININE STREPTOMYCES VINACEUS L-ARGININE OXYGENASE NON-HEME FE(II) HYDROXYLASE CBETA- HYDROXYLATION VIOMYCIN NRPS ALPHA-KETOGLUTARATE OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR THE ERYTHRO-STEREOSPECIFICITY OF THE L-ARGININE OXYGENASE VIOC IN VIOMYCIN BIOSYNTHESIS. FEBS J. V. 276 3669 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG A:1360;
Valid;
none;
submit data
175.209 C6 H15 N4 O2 C(C[C...
FE2 A:1358;
Part of Protein;
none;
submit data
55.845 Fe [Fe+2...
TLA A:1359;
Valid;
none;
submit data
150.087 C4 H6 O6 [C@@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2WBP 1.16 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF VIOC IN COMPLEX WITH FE(II), (2S,3S)- HYDROXYARGININE, AND SUCCINATE STREPTOMYCES VINACEUS OXIDOREDUCTASE NON-HEME FE(II) HYDROXYLASE CBETA-HYDROXYLATION NRPS VIOMYCIN ALPHA-KETOGLUTARATE
Ref.: STRUCTURAL BASIS FOR THE ERYTHRO-STEREOSPECIFICITY OF THE L-ARGININE OXYGENASE VIOC IN VIOMYCIN BIOSYNTHESIS. FEBS J. V. 276 3669 2009
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 318 families.
1 6DAX - HRG C7 H16 N4 O2 C(CCNC(=N)....
2 2WBO - TLA C4 H6 O6 [C@@H]([C@....
3 6ALP - SIN C4 H6 O4 C(CC(=O)O)....
4 2WBP - SIN C4 H6 O4 C(CC(=O)O)....
5 6ALO - OKG C4 H5 O5 C(CC(=O)O[....
6 6MP9 - JX7 C6 H11 N3 O3 [H]/N=C(/N....
7 6ALM - AKG C5 H6 O5 C(CC(=O)O)....
8 6DB2 - SIN C4 H6 O4 C(CC(=O)O)....
9 6ALN - AKG C5 H6 O5 C(CC(=O)O)....
10 6ALQ - SIN C4 H6 O4 C(CC(=O)O)....
11 6MP8 - DAR C6 H15 N4 O2 C(C[C@H](C....
12 6DAZ - SIN C4 H6 O4 C(CC(=O)O)....
13 6ALR - SIN C4 H6 O4 C(CC(=O)O)....
14 2WBQ - ZZU C6 H14 N4 O3 C(CNC(=N)N....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 6DAX - HRG C7 H16 N4 O2 C(CCNC(=N)....
2 2WBO - TLA C4 H6 O6 [C@@H]([C@....
3 6ALP - SIN C4 H6 O4 C(CC(=O)O)....
4 2WBP - SIN C4 H6 O4 C(CC(=O)O)....
5 6ALO - OKG C4 H5 O5 C(CC(=O)O[....
6 6MP9 - JX7 C6 H11 N3 O3 [H]/N=C(/N....
7 6ALM - AKG C5 H6 O5 C(CC(=O)O)....
8 6DB2 - SIN C4 H6 O4 C(CC(=O)O)....
9 6ALN - AKG C5 H6 O5 C(CC(=O)O)....
10 6ALQ - SIN C4 H6 O4 C(CC(=O)O)....
11 6MP8 - DAR C6 H15 N4 O2 C(C[C@H](C....
12 6DAZ - SIN C4 H6 O4 C(CC(=O)O)....
13 6ALR - SIN C4 H6 O4 C(CC(=O)O)....
14 2WBQ - ZZU C6 H14 N4 O3 C(CNC(=N)N....
50% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 6DAX - HRG C7 H16 N4 O2 C(CCNC(=N)....
2 2WBO - TLA C4 H6 O6 [C@@H]([C@....
3 6ALP - SIN C4 H6 O4 C(CC(=O)O)....
4 2WBP - SIN C4 H6 O4 C(CC(=O)O)....
5 6ALO - OKG C4 H5 O5 C(CC(=O)O[....
6 6MP9 - JX7 C6 H11 N3 O3 [H]/N=C(/N....
7 6ALM - AKG C5 H6 O5 C(CC(=O)O)....
8 6DB2 - SIN C4 H6 O4 C(CC(=O)O)....
9 6ALN - AKG C5 H6 O5 C(CC(=O)O)....
10 6ALQ - SIN C4 H6 O4 C(CC(=O)O)....
11 6MP8 - DAR C6 H15 N4 O2 C(C[C@H](C....
12 6DAZ - SIN C4 H6 O4 C(CC(=O)O)....
13 6ALR - SIN C4 H6 O4 C(CC(=O)O)....
14 2WBQ - ZZU C6 H14 N4 O3 C(CNC(=N)N....
15 6DAW - ARG C6 H15 N4 O2 C(C[C@@H](....
16 4M2G - 2OR C6 H15 N4 O4 C([C@H]([C....
17 4M26 - ZZU C6 H14 N4 O3 C(CNC(=N)N....
18 4M2E - HRG C7 H16 N4 O2 C(CCNC(=N)....
19 4M2C - DAR C6 H15 N4 O2 C(C[C@H](C....
20 4M25 - AKG C5 H6 O5 C(CC(=O)O)....
21 4M2F - GGB C5 H12 N4 O3 [H]/N=C(N)....
22 4M27 - ARG C6 H15 N4 O2 C(C[C@@H](....
23 4NE0 - SIN C4 H6 O4 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG; Similar ligands found: 42
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG 1 1
2 DAR 1 1
3 CIR 0.735294 0.763158
4 AAR 0.705882 0.783784
5 ILO 0.615385 0.783784
6 3AR 0.595238 0.891892
7 4JK 0.585366 0.789474
8 NMM 0.585366 0.888889
9 VUR 0.585366 0.810811
10 HAR 0.585366 0.780488
11 VIO 0.581395 0.769231
12 WT2 0.571429 0.805556
13 DA2 0.55814 0.744186
14 2MR 0.545455 0.864865
15 2YH 0.545455 0.65
16 3KJ 0.545455 0.680851
17 1KJ 0.533333 0.744186
18 JM2 0.533333 0.731707
19 NRG 0.521739 0.622642
20 RPI 0.521739 0.64
21 2YJ 0.521739 0.619048
22 API 0.515152 0.611111
23 LN6 0.510638 0.725
24 HRG 0.5 0.941176
25 JM7 0.5 0.731707
26 2KJ 0.489796 0.727273
27 D20 0.489796 0.744186
28 AS1 0.489796 0.8
29 ORN 0.472222 0.757576
30 JM8 0.470588 0.714286
31 JM6 0.470588 0.697674
32 JM4 0.470588 0.697674
33 LYS ARG LYS ARG LYS ARG LYS ARG 0.463415 0.848485
34 MLZ 0.463415 0.65
35 JM5 0.461538 0.714286
36 DLY 0.447368 0.735294
37 DAB 0.441176 0.685714
38 LYS 0.435897 0.764706
39 0TF 0.428571 0.619048
40 2YG 0.42 0.619048
41 PG3 0.416667 0.756757
42 6CL 0.414634 0.638889
Ligand no: 2; Ligand: TLA; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 TAR 1 1
2 TLA 1 1
3 SRT 1 1
4 RAT 0.588235 1
5 LGT 0.588235 1
6 GAE 0.588235 1
7 LAC 0.5 0.611111
8 2OP 0.5 0.611111
9 IPM 0.47619 0.8
10 LFC 0.434783 0.777778
11 ICT 0.416667 0.727273
12 DXX 0.411765 0.777778
13 MAK 0.4 0.941176
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2WBP; Ligand: ARG; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 2wbp.bio1) has 5 residues
No: Leader PDB Ligand Sequence Similarity
1 5B2E MQG 2.94118
2 3GWN FAD 4.38596
3 3KP6 SAL 14.5695
Pocket No.: 2; Query (leader) PDB : 2WBP; Ligand: SIN; Similar sites found with APoc: 173
This union binding pocket(no: 2) in the query (biounit: 2wbp.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 6BU0 IHP None
2 1PTR PRB None
3 5OO5 UUA None
4 5YBN AKG 0.636943
5 4YRD 3IT 1.39665
6 5YJS SAL 1.39665
7 2FCU AKG 1.59744
8 5LY2 OGA 1.67598
9 4IE6 UN9 1.67598
10 2OS2 OGA 1.67598
11 2YBP 2HG 1.67598
12 5FWE OGA 1.67598
13 6H8P OGA 1.67598
14 5LY1 PPI 1.67598
15 5KJW 53C 1.67598
16 2Q8E OGA 1.70455
17 4P7X AKG 1.71233
18 4P7X YCP 1.71233
19 2OQ5 BEN 1.72414
20 1YRO UDP 1.74825
21 4MOB ADP 1.80723
22 5EO8 TFU 1.92926
23 2RG0 CBI 1.95531
24 3OPT AKG 1.95531
25 4RW3 IPD 1.98676
26 5IVE 6E8 2.12121
27 6HKE MLT 2.20126
28 6HKE LMR 2.20126
29 4BXF AKG 2.23464
30 3PUA OGA 2.23464
31 4LIT AKG 2.23464
32 6F5W KG1 2.23464
33 4PEG 5GP 2.23464
34 2X1E X1E 2.2409
35 2WZF BGC 2.51397
36 1VMK GUN 2.52708
37 5JWP AKG 2.55682
38 2Y0I AKG 2.55682
39 3P3N AKG 2.5788
40 2XUM OGA 2.5788
41 1H2K OGA 2.5788
42 1H2M OGA 2.5788
43 4B7E OGA 2.5788
44 4UDK BMA 2.59366
45 5NCJ SIN 2.61194
46 1C3X 8IG 2.63158
47 2JBM SRT 2.67559
48 2D3N GLC GLC GLC 2.7933
49 1OS7 TAU 2.82686
50 1OS7 AKG 2.82686
51 5YBL AKG 2.86624
52 2VAR KDG 2.8754
53 2VAR KDF 2.8754
54 5TV6 PML 2.91667
55 1OI6 TMP 2.92683
56 4QXB OGA 2.94118
57 2GJP MAL 3.07263
58 3MX2 TTP 3.07263
59 2QS8 MET 3.07263
60 4WCX MET 3.07263
61 3GJB AKG 3.1348
62 4XAC AKG 3.1746
63 5L9V OGA 3.1746
64 5DYO FLU 3.30189
65 5ZM4 AKG 3.35196
66 5I8T LAC 3.35196
67 5ZM4 9FU 3.35196
68 2P4S DIH 3.35196
69 1G2O IMH 3.35821
70 5DKK FMN 3.44828
71 5C5T AKG 3.50877
72 1ZZ7 S0H 3.53535
73 3SCH TB6 3.53535
74 5UQD AKG 3.61991
75 6FXR AKG 3.63128
76 1YP4 ADP 3.63128
77 3QDK QDK 3.63128
78 6GNO XDI 3.7037
79 2PR5 FMN 3.78788
80 4DDY DN6 3.80228
81 6ACS CIT 3.87597
82 3N9Q OGA 3.91061
83 3N9O OGA 3.91061
84 3N9P OGA 3.91061
85 3PUR 2HG 3.91061
86 3RKR NAP 3.91061
87 1DNP MHF 3.91061
88 5LUN OGA 3.97727
89 5LUN ARG 3.97727
90 5TFZ 7BC 4
91 1NYW DAU 4.06091
92 3A16 PXO 4.18994
93 4D52 GXL 4.18994
94 5VJE GOS 4.18994
95 1IGW PYR 4.18994
96 3NNF AKG 4.36047
97 4J25 OGA 4.36681
98 4IGQ OGA 4.46927
99 5A1S FLC 4.46927
100 1KAH HIS 4.46927
101 3KV4 OGA 4.7486
102 1GY8 UDP 4.7486
103 5M0T AKG 4.7619
104 3LGS ADE 4.86891
105 3LGS SAH 4.86891
106 2Q37 3AL 4.97238
107 4GK9 MAN BMA MAN MAN MAN 5.01792
108 2UW1 GVM 5.02959
109 3FPF MTA 5.03356
110 3FPF TNA 5.03356
111 4Z7X 3CX 5.04202
112 4OJ8 AKG 5.11945
113 4OJ8 2TQ 5.11945
114 1NX4 AKG 5.12821
115 5V1B 8UY 5.30726
116 1UNB PN1 5.30726
117 1UNB AKG 5.30726
118 5KXE 6Y2 5.34979
119 2IUW AKG 5.46218
120 2WQ4 SFU 5.76923
121 5IFK HPA 5.86592
122 4XMF HSM 5.97826
123 5O9W AKG 6.14525
124 1RJW ETF 6.14525
125 3SAO DBH 6.25
126 1FNZ A2G 6.32911
127 1T66 FLU 6.39269
128 3AVR OGA 6.42458
129 4CP9 GAL CN8 6.61157
130 6F6D AKG 6.70391
131 3QPB URA 6.73759
132 3W21 AKG 6.95971
133 5NXX 3Q7 6.98324
134 6F4T OGA 7.05882
135 3ECN IBM 7.39645
136 5LXB 7A9 7.43802
137 4Y3O OGA 7.5419
138 4CCN OGA 7.5419
139 4CCK OGA 7.5419
140 4CCO OGA 7.5419
141 2VOH CIT 7.64331
142 5D6T NGA 7.72059
143 2A1X AKG 8.10056
144 5EPA AKG 8.24373
145 4BG1 OGA 8.37989
146 4BG1 IVL 8.37989
147 2ARC ARA 9.14634
148 2IXC TRH 9.40594
149 5FLJ QUE 9.67742
150 1L0I PSR 10.2564
151 1RV0 NDG 10.625
152 4QM9 CYS 11.5607
153 1VBO MAN MAN MAN 12.0805
154 4NPL AKG 12.4
155 5N0L ILE 13.2075
156 4RFR RHN 13.3005
157 5TQZ GLC 13.3333
158 5F7J ADE 13.75
159 6GBV FMN 14.3836
160 4OCT AKG 14.4144
161 3KP6 SAL 14.5695
162 5D9G GLU ASN LEU TYR PHE GLN 15.0407
163 5Z84 PEK 16.3265
164 4YG6 GAL NAG 19.0184
165 3LQV ADE 20.5128
166 5I0U DCY 28
167 6F6J CUW 37.1508
168 6F6J SIN 37.1508
169 6EXF LYS 37.9888
170 1DRY AKG 39.6648
171 1DRY AAG 39.6648
172 5L9B AKG 42.1053
173 3HQR OGA 47.0588
Pocket No.: 3; Query (leader) PDB : 2WBP; Ligand: ZZU; Similar sites found with APoc: 173
This union binding pocket(no: 3) in the query (biounit: 2wbp.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 6BU0 IHP None
2 1PTR PRB None
3 5OO5 UUA None
4 5YBN AKG 0.636943
5 4YRD 3IT 1.39665
6 5YJS SAL 1.39665
7 2FCU AKG 1.59744
8 5LY2 OGA 1.67598
9 4IE6 UN9 1.67598
10 2OS2 OGA 1.67598
11 2YBP 2HG 1.67598
12 5FWE OGA 1.67598
13 6H8P OGA 1.67598
14 5LY1 PPI 1.67598
15 5KJW 53C 1.67598
16 2Q8E OGA 1.70455
17 4P7X AKG 1.71233
18 4P7X YCP 1.71233
19 2OQ5 BEN 1.72414
20 1YRO UDP 1.74825
21 4MOB ADP 1.80723
22 5EO8 TFU 1.92926
23 2RG0 CBI 1.95531
24 3OPT AKG 1.95531
25 4RW3 IPD 1.98676
26 5IVE 6E8 2.12121
27 6HKE MLT 2.20126
28 6HKE LMR 2.20126
29 4BXF AKG 2.23464
30 3PUA OGA 2.23464
31 4LIT AKG 2.23464
32 6F5W KG1 2.23464
33 4PEG 5GP 2.23464
34 2X1E X1E 2.2409
35 2WZF BGC 2.51397
36 1VMK GUN 2.52708
37 5JWP AKG 2.55682
38 2Y0I AKG 2.55682
39 3P3N AKG 2.5788
40 2XUM OGA 2.5788
41 1H2K OGA 2.5788
42 1H2M OGA 2.5788
43 4B7E OGA 2.5788
44 4UDK BMA 2.59366
45 5NCJ SIN 2.61194
46 1C3X 8IG 2.63158
47 2JBM SRT 2.67559
48 2D3N GLC GLC GLC 2.7933
49 1OS7 TAU 2.82686
50 1OS7 AKG 2.82686
51 5YBL AKG 2.86624
52 2VAR KDG 2.8754
53 2VAR KDF 2.8754
54 5TV6 PML 2.91667
55 1OI6 TMP 2.92683
56 4QXB OGA 2.94118
57 2GJP MAL 3.07263
58 3MX2 TTP 3.07263
59 2QS8 MET 3.07263
60 4WCX MET 3.07263
61 3GJB AKG 3.1348
62 4XAC AKG 3.1746
63 5L9V OGA 3.1746
64 5DYO FLU 3.30189
65 5ZM4 AKG 3.35196
66 5I8T LAC 3.35196
67 5ZM4 9FU 3.35196
68 2P4S DIH 3.35196
69 1G2O IMH 3.35821
70 5DKK FMN 3.44828
71 5C5T AKG 3.50877
72 1ZZ7 S0H 3.53535
73 3SCH TB6 3.53535
74 5UQD AKG 3.61991
75 6FXR AKG 3.63128
76 1YP4 ADP 3.63128
77 3QDK QDK 3.63128
78 6GNO XDI 3.7037
79 2PR5 FMN 3.78788
80 4DDY DN6 3.80228
81 6ACS CIT 3.87597
82 3N9Q OGA 3.91061
83 3N9O OGA 3.91061
84 3N9P OGA 3.91061
85 3PUR 2HG 3.91061
86 3RKR NAP 3.91061
87 1DNP MHF 3.91061
88 5LUN OGA 3.97727
89 5LUN ARG 3.97727
90 5TFZ 7BC 4
91 1NYW DAU 4.06091
92 3A16 PXO 4.18994
93 4D52 GXL 4.18994
94 5VJE GOS 4.18994
95 1IGW PYR 4.18994
96 3NNF AKG 4.36047
97 4J25 OGA 4.36681
98 4IGQ OGA 4.46927
99 5A1S FLC 4.46927
100 1KAH HIS 4.46927
101 3KV4 OGA 4.7486
102 1GY8 UDP 4.7486
103 5M0T AKG 4.7619
104 3LGS ADE 4.86891
105 3LGS SAH 4.86891
106 2Q37 3AL 4.97238
107 4GK9 MAN BMA MAN MAN MAN 5.01792
108 2UW1 GVM 5.02959
109 3FPF MTA 5.03356
110 3FPF TNA 5.03356
111 4Z7X 3CX 5.04202
112 4OJ8 AKG 5.11945
113 4OJ8 2TQ 5.11945
114 1NX4 AKG 5.12821
115 5V1B 8UY 5.30726
116 1UNB PN1 5.30726
117 1UNB AKG 5.30726
118 5KXE 6Y2 5.34979
119 2IUW AKG 5.46218
120 2WQ4 SFU 5.76923
121 5IFK HPA 5.86592
122 4XMF HSM 5.97826
123 5O9W AKG 6.14525
124 1RJW ETF 6.14525
125 3SAO DBH 6.25
126 1FNZ A2G 6.32911
127 1T66 FLU 6.39269
128 3AVR OGA 6.42458
129 4CP9 GAL CN8 6.61157
130 6F6D AKG 6.70391
131 3QPB URA 6.73759
132 3W21 AKG 6.95971
133 5NXX 3Q7 6.98324
134 6F4T OGA 7.05882
135 3ECN IBM 7.39645
136 5LXB 7A9 7.43802
137 4Y3O OGA 7.5419
138 4CCN OGA 7.5419
139 4CCK OGA 7.5419
140 4CCO OGA 7.5419
141 2VOH CIT 7.64331
142 5D6T NGA 7.72059
143 2A1X AKG 8.10056
144 5EPA AKG 8.24373
145 4BG1 OGA 8.37989
146 4BG1 IVL 8.37989
147 2ARC ARA 9.14634
148 2IXC TRH 9.40594
149 5FLJ QUE 9.67742
150 1L0I PSR 10.2564
151 1RV0 NDG 10.625
152 4QM9 CYS 11.5607
153 1VBO MAN MAN MAN 12.0805
154 4NPL AKG 12.4
155 5N0L ILE 13.2075
156 4RFR RHN 13.3005
157 5TQZ GLC 13.3333
158 5F7J ADE 13.75
159 6GBV FMN 14.3836
160 4OCT AKG 14.4144
161 3KP6 SAL 14.5695
162 5D9G GLU ASN LEU TYR PHE GLN 15.0407
163 5Z84 PEK 16.3265
164 4YG6 GAL NAG 19.0184
165 3LQV ADE 20.5128
166 5I0U DCY 28
167 6F6J CUW 37.1508
168 6F6J SIN 37.1508
169 6EXF LYS 37.9888
170 1DRY AKG 39.6648
171 1DRY AAG 39.6648
172 5L9B AKG 42.1053
173 3HQR OGA 47.0588
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