Receptor
PDB id Resolution Class Description Source Keywords
3DJ8 1.51 Å EC: 3.5.3.1 SYNTHESIS OF (2S)-2-AMINO-7,8-EPOXYOCTANOIC ACID AND STRUCTU METAL-BRIDGING COMPLEX WITH HUMAN ARGINASE I HOMO SAPIENS EPOXIDE BINDING MANGANESE CLUSTER ARGININE METABOLISM DISMUTATION HYDROLASE MANGANESE METAL-BINDING PHOSPHOPROTECYCLE
Ref.: SYNTHESIS OF (2S)-2-AMINO-7,8-EPOXYOCTANOIC ACID AN STRUCTURE OF ITS METAL-BRIDGING COMPLEX WITH HUMAN I ORG.BIOMOL.CHEM. V. 6 3240 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EXY A:650;
B:751;
 Valid;
Valid;
 none;
none;
 submit data
173.21 C8 H15 N O3 C1[C@...
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: EXY; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 EXY 1 1
2 DHH 0.5 0.685714
3 API 0.5 0.611111
4 DLY 0.475 0.638889
5 LYS 0.463415 0.621622
6 NPI 0.452381 0.685714
7 ORN 0.425 0.611111
8 11C 0.404762 0.657143
9 UN1 0.404762 0.657143
Similar Ligands (3D)
Ligand no: 1; Ligand: EXY; Similar ligands found: 181
No: Ligand Similarity coefficient
1 MLY 0.9834
2 ARG 0.9757
3 ABH 0.9664
4 6HN 0.9646
5 HOC 0.9637
6 MLZ 0.9604
7 CIR 0.9578
8 GGB 0.9548
9 ALY 0.9505
10 5AB 0.9458
11 IAR 0.9456
12 DAR 0.9456
13 ILO 0.9455
14 NOT 0.9416
15 HAR 0.9387
16 ZZU 0.9367
17 WT2 0.9358
18 4JK 0.9353
19 M3L 0.9340
20 SLZ 0.9336
21 PML 0.9311
22 FB6 0.9281
23 1PS 0.9278
24 NFZ 0.9270
25 26P 0.9269
26 KAP 0.9266
27 OCA 0.9259
28 HRG 0.9258
29 NNH 0.9257
30 LPA 0.9256
31 N8C 0.9244
32 S2C 0.9235
33 011 0.9206
34 E8U 0.9202
35 8AC 0.9200
36 2NP 0.9196
37 L06 0.9190
38 AHL 0.9184
39 TEG 0.9182
40 GVA 0.9181
41 CUW 0.9180
42 DA2 0.9176
43 KNA 0.9170
44 LPB 0.9167
45 6XA 0.9160
46 3H2 0.9154
47 NMM 0.9151
48 XRX 0.9149
49 FXY 0.9131
50 JX7 0.9121
51 ODI 0.9094
52 2OR 0.9092
53 KPV 0.9086
54 OOG 0.9077
55 VUR 0.9074
56 4TB 0.9060
57 EGV 0.9054
58 XOG 0.9042
59 5PV 0.9040
60 DIA 0.9037
61 DNN 0.9025
62 LYN 0.9025
63 SPD 0.9025
64 ONH 0.9024
65 2FM 0.9015
66 J9Y 0.9014
67 5KJ 0.9012
68 DDK 0.9011
69 7XA 0.9011
70 4DI 0.9008
71 DKA 0.9002
72 9J6 0.9001
73 ENW 0.8992
74 D10 0.8991
75 G3M 0.8980
76 HPL 0.8974
77 SB7 0.8969
78 ENV 0.8965
79 OJD 0.8961
80 OC9 0.8959
81 3GZ 0.8949
82 MGB 0.8948
83 3KJ 0.8935
84 NMH 0.8928
85 OYA 0.8920
86 DDW 0.8919
87 GRQ 0.8916
88 11X 0.8911
89 MHN 0.8905
90 GLY GLY GLY 0.8902
91 RGP 0.8901
92 IJ6 0.8900
93 5TO 0.8900
94 6FG 0.8898
95 PBN 0.8896
96 KPC 0.8892
97 Z70 0.8892
98 7OD 0.8889
99 HPO 0.8889
100 CLT 0.8886
101 MF3 0.8884
102 PRO GLY 0.8882
103 R10 0.8881
104 NWH 0.8876
105 LUQ 0.8876
106 8SZ 0.8870
107 HPN 0.8860
108 JM2 0.8856
109 5OY 0.8854
110 M1T 0.8852
111 9C2 0.8842
112 I38 0.8838
113 FOM 0.8835
114 AZM 0.8832
115 AE3 0.8831
116 37E 0.8829
117 SNR 0.8826
118 6C4 0.8815
119 SSB 0.8814
120 19N 0.8805
121 PA5 0.8793
122 TZP 0.8791
123 4ZD 0.8789
124 58X 0.8787
125 6Q3 0.8785
126 3CX 0.8783
127 JF5 0.8777
128 DTB 0.8776
129 PMV 0.8763
130 F98 0.8760
131 KQY 0.8753
132 AG2 0.8753
133 9YT 0.8751
134 IVL 0.8734
135 AHN 0.8733
136 XRS 0.8731
137 N6C 0.8728
138 3OL 0.8728
139 3OM 0.8728
140 DZA 0.8726
141 9OD 0.8724
142 1HS 0.8723
143 DIR 0.8723
144 OKS 0.8719
145 DHM 0.8716
146 DMA 0.8710
147 R5P 0.8710
148 D53 0.8708
149 0L1 0.8707
150 M5P 0.8699
151 U4G 0.8698
152 HL4 0.8696
153 SB9 0.8695
154 HSA 0.8694
155 A5P 0.8689
156 KPA 0.8676
157 KDG 0.8665
158 A51 0.8653
159 P80 0.8643
160 N9M 0.8640
161 IPR 0.8639
162 TL5 0.8629
163 NRG 0.8625
164 4KJ 0.8624
165 N2Y 0.8622
166 HNE 0.8619
167 FZ3 0.8619
168 5LD 0.8618
169 QFJ 0.8614
170 N9J 0.8593
171 0V7 0.8590
172 5XA 0.8588
173 BTN 0.8578
174 BCH 0.8577
175 4CF 0.8577
176 IJ1 0.8570
177 LT1 0.8568
178 5SP 0.8557
179 JPQ 0.8551
180 OHJ 0.8547
181 6FR 0.8528
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
APoc FAQ
Feedback