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Receptor
PDB id Resolution Class Description Source Keywords
4IXV 2.3 Å EC: 3.5.3.1 CRYSTAL STRUCTURE OF HUMAN ARGINASE-2 COMPLEXED WITH INHIBIT {(5R)-5-AMINO-5-CARBOXY-5-[1-(4-CHLOROBENZYL)PIPERIDIN-4- Y L]PENTYL}(TRIHYDROXY)BORATE(1-) HOMO SAPIENS METALLOENZYME ALPHA/BETA FOLD HYDROLASE ARGININE METABOLIMITOCHONDRION HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: SYNTHESIS OF QUATERNARY ALPHA-AMINO ACID-BASED ARGI INHIBITORS VIA THE UGI REACTION. BIOORG.MED.CHEM.LETT. V. 23 4837 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
XA1 C:405;
A:405;
B:405;
Valid;
Valid;
Valid;
none;
none;
none;
ic50 = 240 nM
399.697 C18 H29 B Cl N2 O5 [B-](...
BME C:404;
A:404;
B:404;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
78.133 C2 H6 O S C(CS)...
MN B:401;
C:401;
A:401;
A:402;
C:402;
B:402;
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...
BEN A:403;
C:403;
B:403;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
120.152 C7 H8 N2 [H]/N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4I06 1.8 Å EC: 3.5.3.1 CRYSTAL STRUCTURE OF HUMAN ARGINASE-2 COMPLEXED WITH INHIBIT HOMO SAPIENS METALLOENZYME ALPHA/BETA FOLD ARGININE METABOLISM HYDROLAMANGANESE MITOCHONDRION
Ref.: DISCOVERY OF (R)-2-AMINO-6-BORONO-2-(2-(PIPERIDIN-1-YL)ETHYL)HEX ACID AND CONGENERS AS HIGHLY POTENT INHIBITORS OF H ARGINASES I AND II FOR TREATMENT OF MYOCARDIAL REPE INJURY. J.MED.CHEM. V. 56 2568 2013
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 4I06 ic50 = 67 nM X8A C14 H30 B N2 O5 [B-](CCCC[....
2 4IXV ic50 = 240 nM XA1 C18 H29 B Cl N2 O5 [B-](CCCC[....
3 4IE3 ic50 = 980 nM 1EE C13 H28 B N2 O6 [B-](CCCC[....
4 4IE2 ic50 = 4500 nM 1EC C9 H21 B N O6 [B-](CCCC[....
5 4HZE ic50 = 1920 nM X7A C13 H28 B N2 O5 [B-](CCCC[....
6 4IXU ic50 = 290 nM 38I C20 H30 B Cl2 N2 O5 [B-](CCCC[....
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: XA1; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 XA1 1 1
2 XA2 0.716216 0.968254
3 38I 0.482759 0.867647
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4I06; Ligand: X8A; Similar sites found with APoc: 22
This union binding pocket(no: 1) in the query (biounit: 4i06.bio3) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 3TTY GLA 1.96078
2 1DFO PLG 1.96078
3 4WXJ GLU 2.23048
4 2VYT MLZ 2.71493
5 3KL3 GCU 2.94118
6 5AYV KPL 3.26797
7 1OFD FMN 3.26797
8 1SQS TLA 3.71901
9 4ZDM GLY 3.83142
10 5T52 NGA 4.13223
11 1Z0N BCD 5.20833
12 4OIT MAN 5.30973
13 6E8I PTR 5.91716
14 6A6A DAL 6.22222
15 4YKI GLY 6.25
16 5D48 L96 6.57895
17 5ECP GSH 7.18954
18 5WKC FAD 7.51634
19 5NE2 DGL 8.16993
20 3RMK BML 8.43373
21 4OX5 DAL 15.508
22 1WOG 16D 38.0328
Pocket No.: 2; Query (leader) PDB : 4I06; Ligand: X8A; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 4i06.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4L80 OXL 1.63399
2 5HRA DAS 2.12766
3 4L9Z OXL 8.55457
Pocket No.: 3; Query (leader) PDB : 4I06; Ligand: X8A; Similar sites found with APoc: 3
This union binding pocket(no: 3) in the query (biounit: 4i06.bio4) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1T0S BML 3.48837
2 1X7D ORN 3.92157
3 5T52 A2G 4.13223
Pocket No.: 4; Query (leader) PDB : 4I06; Ligand: X8A; 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: 4i06.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4I06; Ligand: X8A; 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: 4i06.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4I06; Ligand: X8A; 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: 4i06.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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