Receptor
PDB id Resolution Class Description Source Keywords
3f80 1.6 Å EC: 3.5.3.1 (S)-2-AMINO-6-NITROHEXANOIC ACID BINDS TO HUMAN ARGINASE I THROUGH MULTIPLE NITRO-METAL COORDINATION INTERACTIONS IN T HE BINUCLEAR MANGANESE CLUSTER. RESOLUTION 1.60 A. HOMO SAPIENS NITRONIUM GROUP COORDINATION SURFACE PLASMON RESONANCE ALTERNATIVE SPLICING ARGININE METABOLISM CYTOPLASM DISEASE MUTATION HYDROLASE MANGANESE METAL-BINDING PHOSPHOPROTEIN POLYMORPHISM UREA CYCLE
Ref.: (S)-2-AMINO-6-NITROHEXANOIC ACID BINDS TO HUMAN ARGINASE I THROUGH MULTIPLE NITRO-METAL COORDINATION INTERACTIONS IN THE BINUCLEAR MANGANESE CLUSTER. J.AM.CHEM.SOC. V. 130 17254 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6HN A:551;
A:552;
Valid;
Valid;
none;
none;
Kd = 60 uM
176.17 C6 H12 N2 O4 C(CC[...
MN A:514;
A:515;
B:514;
B:515;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
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
6V7E 1.99 Å EC: 3.5.3.1 HUMAN ARGINASE1 COMPLEXED WITH BICYCLIC INHIBITOR COMPOUND 1 HOMO SAPIENS AGONIST ARG (ARGINASE) BICYCLIC IMMUNOTHERAPY METALLOENZHYDROLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: DISCOVERY AND OPTIMIZATION OF RATIONALLY DESIGNED B INHIBITORS OF HUMAN ARGINASE TO ENHANCE CANCER IMMUNOTHERAPY. ACS MED.CHEM.LETT. V. 11 582 2020
Members (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 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....
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: 6HN; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 6HN 1 1
2 LYS 0.513514 0.604651
3 NPI 0.5 0.619048
4 ABH 0.475 0.62
5 NRG 0.428571 0.696429
6 ONH 0.425 0.688889
7 2JJ 0.425 0.612245
8 5OY 0.425 0.612245
9 NOT 0.422222 0.704545
10 6CL 0.414634 0.619048
11 HAR 0.413043 0.607843
Similar Ligands (3D)
Ligand no: 1; Ligand: 6HN; Similar ligands found: 175
No: Ligand Similarity coefficient
1 ARG 0.9763
2 MLY 0.9720
3 DHH 0.9709
4 EXY 0.9646
5 CIR 0.9628
6 API 0.9609
7 GGB 0.9602
8 ILO 0.9517
9 MLZ 0.9489
10 PML 0.9477
11 E8U 0.9448
12 ENW 0.9443
13 4JK 0.9439
14 WT2 0.9439
15 M3L 0.9439
16 9J6 0.9409
17 OOG 0.9409
18 4TB 0.9399
19 VUR 0.9374
20 26P 0.9371
21 GVA 0.9359
22 S2C 0.9358
23 LPA 0.9331
24 AHL 0.9320
25 JX7 0.9297
26 DAR 0.9291
27 IAR 0.9291
28 TYR 0.9288
29 SLZ 0.9277
30 UN1 0.9263
31 Z70 0.9262
32 9YT 0.9258
33 NMM 0.9226
34 2NP 0.9222
35 5AB 0.9213
36 PBA 0.9212
37 4ZD 0.9208
38 2FM 0.9200
39 TZP 0.9199
40 OCA 0.9192
41 MF3 0.9189
42 LYN 0.9182
43 1PS 0.9182
44 KPV 0.9175
45 HRG 0.9159
46 FB6 0.9151
47 3KJ 0.9151
48 DEZ 0.9150
49 4DI 0.9133
50 L06 0.9133
51 DA2 0.9129
52 SB7 0.9129
53 F98 0.9118
54 JFM 0.9109
55 AHN 0.9105
56 ZZU 0.9101
57 2OR 0.9101
58 CLT 0.9101
59 NNH 0.9097
60 SB9 0.9096
61 J9Y 0.9089
62 XOG 0.9087
63 EGV 0.9066
64 5PV 0.9062
65 XRX 0.9056
66 011 0.9036
67 ENV 0.9030
68 LPB 0.9029
69 ALY 0.9029
70 DXP 0.9020
71 0L1 0.9018
72 JM2 0.9016
73 TEG 0.9008
74 5KJ 0.9007
75 OJD 0.8990
76 GRQ 0.8980
77 PMV 0.8978
78 KAP 0.8976
79 PBN 0.8972
80 3H2 0.8965
81 RGP 0.8963
82 DLY 0.8950
83 KPA 0.8950
84 5LD 0.8947
85 4TP 0.8944
86 CXP 0.8943
87 GNW 0.8939
88 RED 0.8934
89 6C4 0.8932
90 DIR 0.8927
91 5TO 0.8925
92 6FG 0.8924
93 11C 0.8916
94 ENO 0.8911
95 I38 0.8905
96 PRO GLY 0.8904
97 VIO 0.8903
98 LVD 0.8901
99 G3M 0.8900
100 DNN 0.8898
101 FOM 0.8895
102 FXY 0.8892
103 7OD 0.8891
104 NWH 0.8886
105 QFJ 0.8883
106 3YP 0.8881
107 KPC 0.8881
108 CUW 0.8879
109 7UC 0.8879
110 DLT 0.8878
111 HL4 0.8873
112 XRS 0.8869
113 HCI 0.8865
114 KDG 0.8853
115 HPL 0.8852
116 IVL 0.8849
117 KNA 0.8847
118 DZA 0.8842
119 1N5 0.8841
120 4YZ 0.8835
121 N8C 0.8833
122 N9J 0.8817
123 MES 0.8817
124 P93 0.8816
125 PA5 0.8814
126 8AC 0.8810
127 P80 0.8808
128 Q06 0.8807
129 O45 0.8807
130 DKA 0.8803
131 GLY GLY GLY 0.8799
132 1HS 0.8795
133 YOF 0.8788
134 R10 0.8785
135 7BC 0.8784
136 A5P 0.8776
137 JF5 0.8774
138 37E 0.8766
139 IJ6 0.8764
140 LUQ 0.8763
141 DA3 0.8763
142 SPD 0.8758
143 DXG 0.8757
144 ODI 0.8753
145 7C3 0.8745
146 N6C 0.8736
147 SNR 0.8733
148 7XA 0.8720
149 OC9 0.8716
150 8SZ 0.8711
151 5DS 0.8706
152 DED 0.8705
153 KQY 0.8701
154 HPN 0.8698
155 HGA 0.8692
156 NMH 0.8684
157 AE3 0.8681
158 58X 0.8673
159 PO6 0.8672
160 D10 0.8672
161 M5P 0.8669
162 MHN 0.8668
163 LX1 0.8655
164 OYA 0.8642
165 SSB 0.8632
166 5SP 0.8628
167 0A1 0.8624
168 3OL 0.8616
169 3OM 0.8616
170 19N 0.8612
171 DDW 0.8590
172 DER 0.8586
173 D53 0.8562
174 9C2 0.8558
175 LGT 0.8516
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6V7E; Ligand: QRA; 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: 6v7e.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6V7E; Ligand: QRA; 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: 6v7e.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6V7E; Ligand: QRA; 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: 6v7e.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6V7E; Ligand: QRA; Similar sites found with APoc: 3
This union binding pocket(no: 4) in the query (biounit: 6v7e.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 1WOG 16D 39.3443
2 1WOG 16D 39.3443
3 1WOG 16D 39.3443
Pocket No.: 5; Query (leader) PDB : 6V7E; Ligand: QRA; Similar sites found with APoc: 3
This union binding pocket(no: 5) in the query (biounit: 6v7e.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1WOG 16D 39.3443
2 1WOG 16D 39.3443
3 1WOG 16D 39.3443
Pocket No.: 6; Query (leader) PDB : 6V7E; Ligand: QRA; Similar sites found with APoc: 2
This union binding pocket(no: 6) in the query (biounit: 6v7e.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1WOG 16D 39.3443
2 1WOG 16D 39.3443
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