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
6Q39 2.21 Å EC: 3.5.3.1 COMPLEX OF ARGINASE 2 WITH EXAMPLE 49 HOMO SAPIENS METALLOENZYME ALPHA/BETA FOLD HYDROLASE ARGININE METABOLIMANGANESE MITOCHONDRION HYDROLASE-HYDROLASE INHIBITOR COM
Ref.: DISCOVERY OFN-SUBSTITUTED 3-AMINO-4-(3-BORONOPROPYL)PYRROLIDINE-3-CARBOXYLIC HIGHLY POTENT THIRD-GENERATION INHIBITORS OF HUMAN I AND II. J.MED.CHEM. V. 62 8164 2019
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 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 = 509 nM X7A C13 H28 B N2 O5 [B-](CCCC[....
6 6Q37 ic50 = 440 nM HE8 C8 H18 B N2 O5 [B-](CCC[C....
7 6Q39 ic50 = 16 nM HDQ C14 H29 B N3 O5 [B-](CCC[C....
8 4IXU ic50 = 23 nM 38I C20 H30 B Cl2 N2 O5 [B-](CCCC[....
70% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 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 6V7D ic50 = 22 nM QR4 C11 H24 B N2 O5 [B-](CCC[C....
7 4IE1 - 1EC C9 H21 B N O6 [B-](CCCC[....
8 3MFW Ki = 300 uM B3U C6 H10 N4 O2 c1c([nH]c(....
9 3LP4 Kd = 13100 nM LYS C6 H15 N2 O2 C(CC[NH3+]....
10 3GMZ - ORN C5 H12 N2 O2 C(C[C@@H](....
11 4GSZ - ABH C6 H15 B N O5 [B-](CCCC[....
12 3SJT - 5AB C7 H17 B N O5 [B-](CCCC[....
13 2PLL Kd = 5 nM ABH C6 H15 B N O5 [B-](CCCC[....
14 3MFV Ki = 3000 uM Z70 C7 H12 N4 O2 c1c([nH]c(....
15 4GSV - ABH C6 H15 B N O5 [B-](CCCC[....
16 3DJ8 - EXY C8 H15 N O3 C1[C@H](O1....
17 1WVB - S2C C5 H13 B N O5 S [B-](CCSC[....
18 4HWW ic50 = 223 nM X7A C13 H28 B N2 O5 [B-](CCCC[....
19 3E6V Kd = 147 nM ABH C6 H15 B N O5 [B-](CCCC[....
20 3THH - ABH C6 H15 B N O5 [B-](CCCC[....
21 6V7E ic50 = 2 nM QRA C12 H24 B N2 O5 [B-](CCC[C....
22 3LP7 Kd = 3600 nM HAR C6 H14 N4 O3 C(C[C@@H](....
23 2AEB Kd = 5 nM ABH C6 H15 B N O5 [B-](CCCC[....
24 3THJ - ORN C5 H12 N2 O2 C(C[C@@H](....
25 6V7F ic50 = 14 nM QRJ C12 H26 B N2 O5 [B-](CCC[C....
26 3F80 Kd = 60 uM 6HN C6 H12 N2 O4 C(CC[N+](=....
27 3E6K Kd = 7000 nM ABH C6 H15 B N O5 [B-](CCCC[....
28 4HXQ ic50 = 60 nM X8A C14 H30 B N2 O5 [B-](CCCC[....
29 4GWD - ABH C6 H15 B N O5 [B-](CCCC[....
30 6V7C ic50 = 29 nM QR1 C11 H24 B N2 O5 [B-](CCC[C....
31 4I06 ic50 = 67 nM X8A C14 H30 B N2 O5 [B-](CCCC[....
32 4IXV ic50 = 240 nM XA1 C18 H29 B Cl N2 O5 [B-](CCCC[....
33 4IE3 ic50 = 980 nM 1EE C13 H28 B N2 O6 [B-](CCCC[....
34 4IE2 ic50 = 4500 nM 1EC C9 H21 B N O6 [B-](CCCC[....
35 4HZE ic50 = 509 nM X7A C13 H28 B N2 O5 [B-](CCCC[....
36 6Q37 ic50 = 440 nM HE8 C8 H18 B N2 O5 [B-](CCC[C....
37 6Q39 ic50 = 16 nM HDQ C14 H29 B N3 O5 [B-](CCC[C....
38 4IXU ic50 = 23 nM 38I C20 H30 B Cl2 N2 O5 [B-](CCCC[....
39 1T5G - ARG C6 H15 N4 O2 C(C[C@@H](....
40 1D3V Kd = 0.11 uM ABH C6 H15 B N O5 [B-](CCCC[....
41 1HQG - ORN C5 H12 N2 O2 C(C[C@@H](....
42 1T4T ic50 < 400 uM DIR C4 H10 N4 O3 C([C@@H](C....
43 1T5F Ki = 60 uM DHH C7 H15 N O4 C(CCC(O)O)....
44 1P8R - S2C C5 H13 B N O5 S [B-](CCSC[....
45 1HQ5 Kd = 2.22 uM S2C C5 H13 B N O5 S [B-](CCSC[....
46 3E9B Ki = 4500 nM S2C C5 H13 B N O5 S [B-](CCSC[....
50% Homology Family (61)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 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 6V7D ic50 = 22 nM QR4 C11 H24 B N2 O5 [B-](CCC[C....
14 4IE1 - 1EC C9 H21 B N O6 [B-](CCCC[....
15 3MFW Ki = 300 uM B3U C6 H10 N4 O2 c1c([nH]c(....
16 3LP4 Kd = 13100 nM LYS C6 H15 N2 O2 C(CC[NH3+]....
17 3GMZ - ORN C5 H12 N2 O2 C(C[C@@H](....
18 4GSZ - ABH C6 H15 B N O5 [B-](CCCC[....
19 3SJT - 5AB C7 H17 B N O5 [B-](CCCC[....
20 2PLL Kd = 5 nM ABH C6 H15 B N O5 [B-](CCCC[....
21 3MFV Ki = 3000 uM Z70 C7 H12 N4 O2 c1c([nH]c(....
22 4GSV - ABH C6 H15 B N O5 [B-](CCCC[....
23 3DJ8 - EXY C8 H15 N O3 C1[C@H](O1....
24 1WVB - S2C C5 H13 B N O5 S [B-](CCSC[....
25 4HWW ic50 = 223 nM X7A C13 H28 B N2 O5 [B-](CCCC[....
26 3E6V Kd = 147 nM ABH C6 H15 B N O5 [B-](CCCC[....
27 3THH - ABH C6 H15 B N O5 [B-](CCCC[....
28 6V7E ic50 = 2 nM QRA C12 H24 B N2 O5 [B-](CCC[C....
29 3LP7 Kd = 3600 nM HAR C6 H14 N4 O3 C(C[C@@H](....
30 2AEB Kd = 5 nM ABH C6 H15 B N O5 [B-](CCCC[....
31 3THJ - ORN C5 H12 N2 O2 C(C[C@@H](....
32 6V7F ic50 = 14 nM QRJ C12 H26 B N2 O5 [B-](CCC[C....
33 3F80 Kd = 60 uM 6HN C6 H12 N2 O4 C(CC[N+](=....
34 3E6K Kd = 7000 nM ABH C6 H15 B N O5 [B-](CCCC[....
35 4HXQ ic50 = 60 nM X8A C14 H30 B N2 O5 [B-](CCCC[....
36 4GWD - ABH C6 H15 B N O5 [B-](CCCC[....
37 6V7C ic50 = 29 nM QR1 C11 H24 B N2 O5 [B-](CCC[C....
38 4I06 ic50 = 67 nM X8A C14 H30 B N2 O5 [B-](CCCC[....
39 4IXV ic50 = 240 nM XA1 C18 H29 B Cl N2 O5 [B-](CCCC[....
40 4IE3 ic50 = 980 nM 1EE C13 H28 B N2 O6 [B-](CCCC[....
41 4IE2 ic50 = 4500 nM 1EC C9 H21 B N O6 [B-](CCCC[....
42 4HZE ic50 = 509 nM X7A C13 H28 B N2 O5 [B-](CCCC[....
43 6Q37 ic50 = 440 nM HE8 C8 H18 B N2 O5 [B-](CCC[C....
44 6Q39 ic50 = 16 nM HDQ C14 H29 B N3 O5 [B-](CCC[C....
45 4IXU ic50 = 23 nM 38I C20 H30 B Cl2 N2 O5 [B-](CCCC[....
46 4IU4 Ki ~ 10 uM S2C C5 H13 B N O5 S [B-](CCSC[....
47 4IU1 Ki ~ 50 uM NNH C5 H12 N4 O3 [H]/N=C(/N....
48 4IU5 - ORN C5 H12 N2 O2 C(C[C@@H](....
49 4IU0 Ki = 1.3 uM ABH C6 H15 B N O5 [B-](CCCC[....
50 1T5G - ARG C6 H15 N4 O2 C(C[C@@H](....
51 1D3V Kd = 0.11 uM ABH C6 H15 B N O5 [B-](CCCC[....
52 1HQG - ORN C5 H12 N2 O2 C(C[C@@H](....
53 1T4T ic50 < 400 uM DIR C4 H10 N4 O3 C([C@@H](C....
54 1T5F Ki = 60 uM DHH C7 H15 N O4 C(CCC(O)O)....
55 1P8R - S2C C5 H13 B N O5 S [B-](CCSC[....
56 1HQ5 Kd = 2.22 uM S2C C5 H13 B N O5 S [B-](CCSC[....
57 3E9B Ki = 4500 nM S2C C5 H13 B N O5 S [B-](CCSC[....
58 5ZEE - HAR C6 H14 N4 O3 C(C[C@@H](....
59 5ZEF - NVA C5 H11 N O2 CCC[C@@H](....
60 5CEV - LYS C6 H15 N2 O2 C(CC[NH3+]....
61 3CEV - ARG C6 H15 N4 O2 C(C[C@@H](....
Polypharmacology
Similar Ligands (2D)
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 Ligands (3D)
Ligand no: 1; Ligand: XA1; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6Q39; Ligand: HDQ; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 6q39.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1WOG 16D 38.0328
2 1WOG 16D 38.0328
3 1WOG 16D 38.0328
Pocket No.: 2; Query (leader) PDB : 6Q39; Ligand: HDQ; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 6q39.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1WOG 16D 38.0328
2 1WOG 16D 38.0328
3 1WOG 16D 38.0328
Pocket No.: 3; Query (leader) PDB : 6Q39; Ligand: HDQ; Similar sites found with APoc: 3
This union binding pocket(no: 3) in the query (biounit: 6q39.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1WOG 16D 38.0328
2 1WOG 16D 38.0328
3 1WOG 16D 38.0328
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