Receptor
PDB id Resolution Class Description Source Keywords
1T5G 2.4 Å EC: 3.5.3.1 ARGINASE-F2-L-ARGININE COMPLEX RATTUS NORVEGICUS ARGINASE L-ARGININE FLUORIDE IONS HYDROLASE
Ref.: INHIBITOR COORDINATION INTERACTIONS IN THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE BIOCHEMISTRY V. 43 8987 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG A:1000;
B:1001;
C:1002;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
175.209 C6 H15 N4 O2 C(C[C...
F A:602;
A:603;
B:604;
B:605;
C:600;
C:601;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
18.998 F [F-]
MN A:500;
A:501;
B:502;
B:503;
C:504;
C:505;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1D3V 1.7 Å EC: 3.5.3.1 CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, A N L-ARGININE ANALOG RATTUS NORVEGICUS BINUCLEAR MANGANESE CLUSTER BORONIC ACID INHIBITOR PERFECTLY TWINNED CRYSTAL HYDROLASE
Ref.: ARGINASE-BORONIC ACID COMPLEX HIGHLIGHTS A PHYSIOLOGICAL ROLE IN ERECTILE FUNCTION. NAT.STRUCT.BIOL. V. 6 1043 1999
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1T5G - ARG C6 H15 N4 O2 C(C[C@@H](....
2 1D3V Kd = 0.11 uM ABH C6 H15 B N O5 [B-](CCCC[....
3 1HQG - ORN C5 H12 N2 O2 C(C[C@@H](....
4 1T4T ic50 < 400 uM DIR C4 H10 N4 O3 C([C@@H](C....
5 1T5F Ki ~ 60 uM DHH C7 H15 N O4 C(CCC(O)O)....
6 1P8R - S2C C5 H13 B N O5 S [B-](CCSC[....
7 1HQ5 Kd = 2.22 uM S2C C5 H13 B N O5 S [B-](CCSC[....
8 3E9B Ki = 4500 nM S2C C5 H13 B N O5 S [B-](CCSC[....
70% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3SKK - 4U7 C7 H15 B F2 N O5 [B-](CCCC[....
2 3GN0 Ki = 3.9 mM DMO C6 H12 F2 N2 O2 C(CC(C(F)F....
3 1WVA Kd = 270 nM S2C C5 H13 B N O5 S [B-](CCSC[....
4 3KV2 Kd = 47.51 nM NNH C5 H12 N4 O3 [H]/N=C(/N....
5 2PHO Kd > 0.1 mM TSZ C H5 N3 S C(=S)(N)NN
6 4IE1 - 1EC C9 H21 B N O6 [B-](CCCC[....
7 3MFW Ki = 300 uM B3U C6 H10 N4 O2 c1c([nH]c(....
8 3LP4 Kd = 13100 nM LYS C6 H15 N2 O2 C(CC[NH3+]....
9 3GMZ - ORN C5 H12 N2 O2 C(C[C@@H](....
10 4GSZ - ABH C6 H15 B N O5 [B-](CCCC[....
11 3SJT - 5AB C7 H17 B N O5 [B-](CCCC[....
12 2PLL Kd = 5 nM ABH C6 H15 B N O5 [B-](CCCC[....
13 3MFV Ki = 3000 uM Z70 C7 H12 N4 O2 c1c([nH]c(....
14 4GSV - ABH C6 H15 B N O5 [B-](CCCC[....
15 3DJ8 - EXY C8 H15 N O3 C1[C@H](O1....
16 1WVB - S2C C5 H13 B N O5 S [B-](CCSC[....
17 4HWW ic50 = 1450 nM X7A C13 H28 B N2 O5 [B-](CCCC[....
18 3E6V Kd = 147 nM ABH C6 H15 B N O5 [B-](CCCC[....
19 3THH - ABH C6 H15 B N O5 [B-](CCCC[....
20 3LP7 Kd = 3600 nM HAR C6 H14 N4 O3 C(C[C@@H](....
21 2AEB Kd = 5 nM ABH C6 H15 B N O5 [B-](CCCC[....
22 3THJ - ORN C5 H12 N2 O2 C(C[C@@H](....
23 3F80 Kd = 60 uM 6HN C6 H12 N2 O4 C(CC[N+](=....
24 3E6K Kd = 7000 nM ABH C6 H15 B N O5 [B-](CCCC[....
25 4HXQ ic50 = 60 nM X8A C14 H30 B N2 O5 [B-](CCCC[....
26 4GWD - ABH C6 H15 B N O5 [B-](CCCC[....
27 4I06 ic50 = 67 nM X8A C14 H30 B N2 O5 [B-](CCCC[....
28 4IXV ic50 = 240 nM XA1 C18 H29 B Cl N2 O5 [B-](CCCC[....
29 4IE3 ic50 = 980 nM 1EE C13 H28 B N2 O6 [B-](CCCC[....
30 4IE2 ic50 = 4500 nM 1EC C9 H21 B N O6 [B-](CCCC[....
31 4HZE ic50 = 1920 nM X7A C13 H28 B N2 O5 [B-](CCCC[....
32 4IXU ic50 = 290 nM 38I C20 H30 B Cl2 N2 O5 [B-](CCCC[....
33 1T5G - ARG C6 H15 N4 O2 C(C[C@@H](....
34 1D3V Kd = 0.11 uM ABH C6 H15 B N O5 [B-](CCCC[....
35 1HQG - ORN C5 H12 N2 O2 C(C[C@@H](....
36 1T4T ic50 < 400 uM DIR C4 H10 N4 O3 C([C@@H](C....
37 1T5F Ki ~ 60 uM DHH C7 H15 N O4 C(CCC(O)O)....
38 1P8R - S2C C5 H13 B N O5 S [B-](CCSC[....
39 1HQ5 Kd = 2.22 uM S2C C5 H13 B N O5 S [B-](CCSC[....
40 3E9B Ki = 4500 nM S2C C5 H13 B N O5 S [B-](CCSC[....
50% Homology Family (53)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4Q3S Kd = 0.26 uM X7A C13 H28 B N2 O5 [B-](CCCC[....
2 4Q42 - ORN C5 H12 N2 O2 C(C[C@@H](....
3 4Q40 - VAL C5 H11 N O2 CC(C)[C@@H....
4 4Q3U Kd = 0.36 uM NNH C5 H12 N4 O3 [H]/N=C(/N....
5 4Q41 - LYS C6 H15 N2 O2 C(CC[NH3+]....
6 4Q3Q Kd = 1.3 uM ABH C6 H15 B N O5 [B-](CCCC[....
7 4Q3T Kd = 0.33 uM HAR C6 H14 N4 O3 C(C[C@@H](....
8 3SKK - 4U7 C7 H15 B F2 N O5 [B-](CCCC[....
9 3GN0 Ki = 3.9 mM DMO C6 H12 F2 N2 O2 C(CC(C(F)F....
10 1WVA Kd = 270 nM S2C C5 H13 B N O5 S [B-](CCSC[....
11 3KV2 Kd = 47.51 nM NNH C5 H12 N4 O3 [H]/N=C(/N....
12 2PHO Kd > 0.1 mM TSZ C H5 N3 S C(=S)(N)NN
13 4IE1 - 1EC C9 H21 B N O6 [B-](CCCC[....
14 3MFW Ki = 300 uM B3U C6 H10 N4 O2 c1c([nH]c(....
15 3LP4 Kd = 13100 nM LYS C6 H15 N2 O2 C(CC[NH3+]....
16 3GMZ - ORN C5 H12 N2 O2 C(C[C@@H](....
17 4GSZ - ABH C6 H15 B N O5 [B-](CCCC[....
18 3SJT - 5AB C7 H17 B N O5 [B-](CCCC[....
19 2PLL Kd = 5 nM ABH C6 H15 B N O5 [B-](CCCC[....
20 3MFV Ki = 3000 uM Z70 C7 H12 N4 O2 c1c([nH]c(....
21 4GSV - ABH C6 H15 B N O5 [B-](CCCC[....
22 3DJ8 - EXY C8 H15 N O3 C1[C@H](O1....
23 1WVB - S2C C5 H13 B N O5 S [B-](CCSC[....
24 4HWW ic50 = 1450 nM X7A C13 H28 B N2 O5 [B-](CCCC[....
25 3E6V Kd = 147 nM ABH C6 H15 B N O5 [B-](CCCC[....
26 3THH - ABH C6 H15 B N O5 [B-](CCCC[....
27 3LP7 Kd = 3600 nM HAR C6 H14 N4 O3 C(C[C@@H](....
28 2AEB Kd = 5 nM ABH C6 H15 B N O5 [B-](CCCC[....
29 3THJ - ORN C5 H12 N2 O2 C(C[C@@H](....
30 3F80 Kd = 60 uM 6HN C6 H12 N2 O4 C(CC[N+](=....
31 3E6K Kd = 7000 nM ABH C6 H15 B N O5 [B-](CCCC[....
32 4HXQ ic50 = 60 nM X8A C14 H30 B N2 O5 [B-](CCCC[....
33 4GWD - ABH C6 H15 B N O5 [B-](CCCC[....
34 4I06 ic50 = 67 nM X8A C14 H30 B N2 O5 [B-](CCCC[....
35 4IXV ic50 = 240 nM XA1 C18 H29 B Cl N2 O5 [B-](CCCC[....
36 4IE3 ic50 = 980 nM 1EE C13 H28 B N2 O6 [B-](CCCC[....
37 4IE2 ic50 = 4500 nM 1EC C9 H21 B N O6 [B-](CCCC[....
38 4HZE ic50 = 1920 nM X7A C13 H28 B N2 O5 [B-](CCCC[....
39 4IXU ic50 = 290 nM 38I C20 H30 B Cl2 N2 O5 [B-](CCCC[....
40 4IU4 Ki ~ 10 uM S2C C5 H13 B N O5 S [B-](CCSC[....
41 4IU1 Ki ~ 50 uM NNH C5 H12 N4 O3 [H]/N=C(/N....
42 4IU5 - ORN C5 H12 N2 O2 C(C[C@@H](....
43 4IU0 Ki = 1.3 uM ABH C6 H15 B N O5 [B-](CCCC[....
44 1T5G - ARG C6 H15 N4 O2 C(C[C@@H](....
45 1D3V Kd = 0.11 uM ABH C6 H15 B N O5 [B-](CCCC[....
46 1HQG - ORN C5 H12 N2 O2 C(C[C@@H](....
47 1T4T ic50 < 400 uM DIR C4 H10 N4 O3 C([C@@H](C....
48 1T5F Ki ~ 60 uM DHH C7 H15 N O4 C(CCC(O)O)....
49 1P8R - S2C C5 H13 B N O5 S [B-](CCSC[....
50 1HQ5 Kd = 2.22 uM S2C C5 H13 B N O5 S [B-](CCSC[....
51 3E9B Ki = 4500 nM S2C C5 H13 B N O5 S [B-](CCSC[....
52 5CEV - LYS C6 H15 N2 O2 C(CC[NH3+]....
53 3CEV - ARG C6 H15 N4 O2 C(C[C@@H](....
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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1D3V; Ligand: ABH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1d3v.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1D3V; Ligand: ABH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1d3v.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1D3V; Ligand: ABH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1d3v.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1D3V; Ligand: ABH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1d3v.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1D3V; Ligand: ABH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1d3v.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1D3V; Ligand: ABH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1d3v.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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