Receptor
PDB id Resolution Class Description Source Keywords
5ZEE 1.74 Å EC: 3.5.3.1 CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA ARGINASE IN COMPL N(OMEGA)-HYDROXY-L-ARGININE (NOHA) AT 1.74 A ENTAMOEBA HISTOLYTICA METALLOENZYME HYDROLASE-INHIBITOR COMPLEX
Ref.: STRUCTURAL INSIGHTS INTO ENTAMOEBA HISTOLYTICA ARGI STRUCTURE-BASED IDENTIFICATION OF NOVEL NON-AMINO A INHIBITORS AS POTENTIAL ANTIAMOEBIC MOLECULES. FEBS J. V. 286 4135 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MN B:303;
A:303;
A:302;
B:302;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
EDO A:307;
A:306;
A:305;
A:304;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
HAR A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
190.2 C6 H14 N4 O3 C(C[C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ZEE 1.74 Å EC: 3.5.3.1 CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA ARGINASE IN COMPL N(OMEGA)-HYDROXY-L-ARGININE (NOHA) AT 1.74 A ENTAMOEBA HISTOLYTICA METALLOENZYME HYDROLASE-INHIBITOR COMPLEX
Ref.: STRUCTURAL INSIGHTS INTO ENTAMOEBA HISTOLYTICA ARGI STRUCTURE-BASED IDENTIFICATION OF NOVEL NON-AMINO A INHIBITORS AS POTENTIAL ANTIAMOEBIC MOLECULES. FEBS J. V. 286 4135 2019
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 5ZEH - ORN C5 H12 N2 O2 C(C[C@@H](....
2 5ZEE - HAR C6 H14 N4 O3 C(C[C@@H](....
3 5ZEF - NVA C5 H11 N O2 CCC[C@@H](....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5ZEH - ORN C5 H12 N2 O2 C(C[C@@H](....
2 5ZEE - HAR C6 H14 N4 O3 C(C[C@@H](....
3 5ZEF - NVA C5 H11 N O2 CCC[C@@H](....
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: HAR; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 HAR 1 1
2 NMM 0.707317 0.744186
3 NRG 0.666667 0.722222
4 NNH 0.65 0.928571
5 1KJ 0.644444 0.906977
6 RPI 0.630435 0.711538
7 ILO 0.619048 0.659091
8 CIR 0.6 0.681818
9 2KJ 0.591837 0.886364
10 D20 0.591837 0.673469
11 AS1 0.591837 0.717391
12 4JK 0.590909 0.704545
13 VUR 0.590909 0.681818
14 DAR 0.585366 0.780488
15 ARG 0.585366 0.780488
16 WT2 0.577778 0.714286
17 DA2 0.565217 0.64
18 3KJ 0.553191 0.829787
19 ONH 0.55 0.804878
20 JM2 0.541667 0.625
21 LN6 0.52 0.617021
22 HRG 0.511111 0.780488
23 JM7 0.509804 0.625
24 JM4 0.509434 0.6
25 3AR 0.5 0.711111
26 VIO 0.489796 0.617021
27 2MR 0.489796 0.727273
28 JM8 0.481481 0.612245
29 JM6 0.481481 0.6
30 JM5 0.472727 0.612245
31 AHL 0.468085 0.787234
32 5KJ 0.431373 0.78
33 BHH 0.428571 0.772727
34 ORN 0.414634 0.625
35 6HN 0.413043 0.607843
36 AAR 0.4 0.622222
Similar Ligands (3D)
Ligand no: 1; Ligand: HAR; Similar ligands found: 232
No: Ligand Similarity coefficient
1 GGB 0.9697
2 ABH 0.9597
3 MLY 0.9572
4 NPI 0.9442
5 KPV 0.9398
6 EXY 0.9387
7 FB6 0.9352
8 DNN 0.9350
9 IAR 0.9342
10 DHH 0.9340
11 MLZ 0.9310
12 26P 0.9307
13 EGV 0.9293
14 Z70 0.9280
15 M3L 0.9279
16 4KJ 0.9264
17 SB7 0.9253
18 LPA 0.9248
19 JGY 0.9242
20 J9Y 0.9233
21 5AB 0.9230
22 S2C 0.9223
23 NOT 0.9223
24 5PV 0.9222
25 TEG 0.9205
26 SB9 0.9188
27 API 0.9179
28 6FG 0.9174
29 E8U 0.9163
30 ENW 0.9160
31 2OR 0.9158
32 PML 0.9144
33 2NP 0.9142
34 GVA 0.9127
35 I58 0.9127
36 2J3 0.9122
37 4ZD 0.9121
38 HJD 0.9118
39 KAP 0.9110
40 ALY 0.9110
41 XI7 0.9109
42 ENV 0.9107
43 11X 0.9088
44 MKN 0.9087
45 ZZU 0.9085
46 NFZ 0.9084
47 SZ7 0.9084
48 OCA 0.9084
49 6C5 0.9072
50 KNA 0.9072
51 DKA 0.9072
52 RGP 0.9066
53 19N 0.9062
54 8AC 0.9057
55 7XA 0.9054
56 S0B 0.9050
57 3GZ 0.9038
58 BZM 0.9037
59 IJ6 0.9036
60 G3M 0.9033
61 JX7 0.9025
62 M5P 0.9022
63 P93 0.9021
64 4Z0 0.9015
65 9J6 0.9008
66 JF5 0.9006
67 OJD 0.9004
68 KLS 0.8995
69 5TO 0.8994
70 9YT 0.8982
71 XOG 0.8979
72 FZ3 0.8977
73 6C9 0.8976
74 1PS 0.8974
75 6C4 0.8974
76 58X 0.8974
77 OOG 0.8973
78 4DI 0.8971
79 LL2 0.8969
80 N8C 0.8959
81 UN1 0.8949
82 D53 0.8947
83 DTB 0.8938
84 IJ1 0.8937
85 S0F 0.8932
86 3CX 0.8930
87 0V7 0.8930
88 PRO GLY 0.8930
89 SPD 0.8923
90 A51 0.8921
91 0QA 0.8920
92 0XR 0.8916
93 TPM 0.8912
94 D4G 0.8909
95 AOY 0.8908
96 GHQ 0.8905
97 GRQ 0.8903
98 GGG 0.8900
99 LVD 0.8898
100 HLP 0.8897
101 MVH 0.8891
102 3S9 0.8890
103 A8K 0.8889
104 TBJ 0.8888
105 AHN 0.8885
106 3IP 0.8885
107 PHQ ALA 0.8877
108 8YH 0.8872
109 011 0.8868
110 DA3 0.8868
111 OKP 0.8865
112 PQV 0.8858
113 YOF 0.8854
114 4TB 0.8848
115 PZX 0.8844
116 4YZ 0.8840
117 9OD 0.8837
118 1HS 0.8837
119 1HR 0.8822
120 S7D 0.8818
121 3YP 0.8817
122 DI9 0.8816
123 7MW 0.8814
124 2FM 0.8811
125 MGB 0.8806
126 DHM 0.8802
127 AZM 0.8802
128 ODI 0.8801
129 A7Q 0.8795
130 FHV 0.8795
131 64Z 0.8791
132 YIP 0.8787
133 D10 0.8781
134 IYR 0.8781
135 MF3 0.8778
136 8CV 0.8773
137 27K 0.8771
138 JFM 0.8770
139 0OP 0.8770
140 M5B 0.8769
141 DX5 0.8769
142 CT0 0.8764
143 6MW 0.8760
144 3GC 0.8760
145 PA5 0.8760
146 SLZ 0.8759
147 YE6 0.8754
148 GLY GLY GLY 0.8754
149 DBE 0.8753
150 N2Y 0.8749
151 F98 0.8749
152 4FP 0.8747
153 OJM 0.8743
154 BSU 0.8743
155 DZA 0.8741
156 PUE 0.8740
157 0L1 0.8739
158 AX5 0.8738
159 ZE7 0.8734
160 KPC 0.8734
161 HPK 0.8732
162 TZP 0.8732
163 IPE 0.8728
164 RP3 0.8725
165 STV 0.8721
166 N9M 0.8719
167 RE4 0.8719
168 E79 0.8711
169 3H2 0.8711
170 SS9 0.8698
171 PBN 0.8697
172 DIA 0.8697
173 5UF 0.8697
174 GAE 0.8696
175 HPX 0.8692
176 4Z1 0.8690
177 4TP 0.8689
178 VFG 0.8688
179 S0A 0.8687
180 A9B 0.8687
181 0K7 0.8685
182 5DS 0.8685
183 HL6 0.8685
184 FXY 0.8684
185 9VQ 0.8682
186 HPL 0.8681
187 A98 0.8680
188 6L6 0.8676
189 PMV 0.8675
190 E4P 0.8673
191 HPO 0.8673
192 37E 0.8671
193 STL 0.8665
194 DXP 0.8660
195 L06 0.8659
196 R10 0.8657
197 HPZ 0.8651
198 HX8 0.8651
199 BZQ 0.8650
200 A5P 0.8647
201 IPR 0.8647
202 YIH 0.8646
203 LYS 0.8643
204 KYN 0.8634
205 D2G 0.8629
206 N9J 0.8624
207 CXP 0.8616
208 PUW 0.8611
209 7N8 0.8609
210 TZM 0.8597
211 TYR 0.8596
212 TMG 0.8595
213 MD6 0.8590
214 BL0 0.8580
215 94X 0.8579
216 NK5 0.8576
217 5O5 0.8575
218 SNR 0.8574
219 CCW 0.8567
220 M2E 0.8566
221 0OY 0.8563
222 11C 0.8562
223 7VY 0.8559
224 0OL 0.8556
225 9JH 0.8555
226 F02 0.8546
227 2JJ 0.8544
228 JVD 0.8543
229 6J5 0.8539
230 5SP 0.8533
231 G6Q 0.8529
232 OC9 0.8523
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ZEE; Ligand: HAR; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 5zee.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1WOG 16D 27.541
2 1WOG 16D 27.541
Pocket No.: 2; Query (leader) PDB : 5ZEE; Ligand: HAR; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 5zee.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1WOG 16D 27.541
2 1WOG 16D 27.541
3 1WOG 16D 27.541
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