Receptor
PDB id Resolution Class Description Source Keywords
4hzm 1.45 Å EC: 3.2.1.52 CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM FAMILY 3 GLYCOSI HYDROLASE (NAGZ) BOUND TO N-[(3S,4R,5R,6R)-4,5-DIHYDROXY-6-( HYDROXYMETHYL)PIPERIDIN-3-YL]BUTANAMIDE SALMONELLA ENTERICA SUBSP. ENTERICA SETYPHIMURIUM TIM-BARREL HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: THE DEVELOPMENT OF SELECTIVE INHIBITORS OF NAGZ: IN SUSCEPTIBILITY OF GRAM-NEGATIVE BACTERIA TO BETA-LA CHEMBIOCHEM V. 14 1973 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1BW B:401;
A:400;
Valid;
Valid;
none;
none;
Ki = 23.2 uM
232.277 C10 H20 N2 O4 CCCC(...
MES B:402;
Invalid;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4GVF 1.35 Å EC: 3.2.1.52 CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM FAMILY 3 GLYCOSI HYDROLASE (NAGZ) BOUND TO GLCNAC SALMONELLA ENTERICA SUBSP. ENTERICA SETYPHIMURIUM TIM-BARREL HYDROLASE
Ref.: ACTIVE SITE PLASTICITY WITHIN THE GLYCOSIDE HYDROLA UNDERLIES A DYNAMIC MECHANISM OF SUBSTRATE DISTORTI CHEM.BIOL. V. 19 1471 2012
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 4GVF - NAG C8 H15 N O6 CC(=O)N[C@....
2 4GVI - NAG AH0 n/a n/a
3 4HZM Ki = 23.2 uM 1BW C10 H20 N2 O4 CCCC(=O)N[....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 4GVF - NAG C8 H15 N O6 CC(=O)N[C@....
2 4GVI - NAG AH0 n/a n/a
3 4HZM Ki = 23.2 uM 1BW C10 H20 N2 O4 CCCC(=O)N[....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 5UTQ Ki = 0.05 uM OAN C15 H19 N3 O7 CC(=O)N[C@....
2 5UTP Ki = 3 uM 8M7 C19 H27 N3 O7 CCC(CC)C(=....
3 4MSS Ki = 3.6 uM 2CZ C8 H16 N2 O4 CC(=O)N[C@....
4 5UTR Kd = 7 uM 8MP C10 H20 N2 O4 CCCC(=O)N[....
5 3GSM - VPU C18 H25 N3 O7 CCCCC(=O)N....
6 2OXN Ki = 0.036 uM OAN C15 H19 N3 O7 CC(=O)N[C@....
7 3GS6 - NP6 C17 H23 N3 O7 CCCC(=O)N[....
8 1Y65 - NAG C8 H15 N O6 CC(=O)N[C@....
9 4GVF - NAG C8 H15 N O6 CC(=O)N[C@....
10 4GVI - NAG AH0 n/a n/a
11 4HZM Ki = 23.2 uM 1BW C10 H20 N2 O4 CCCC(=O)N[....
12 5G3R - NAG C8 H15 N O6 CC(=O)N[C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 1BW; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 1BW 1 1
2 NOK 0.632653 0.882353
3 DJN 0.632653 0.882353
4 8MP 0.584906 0.884615
Similar Ligands (3D)
Ligand no: 1; Ligand: 1BW; Similar ligands found: 266
No: Ligand Similarity coefficient
1 BGN 0.9638
2 VPU 0.9457
3 STZ 0.9436
4 YX1 0.9436
5 NAG 0.9316
6 AJG 0.9282
7 7EH 0.9209
8 HBI 0.9205
9 1FE 0.9188
10 B41 0.9173
11 Y3L 0.9171
12 NDG 0.9161
13 PLP 0.9149
14 QIV 0.9148
15 MUR 0.9145
16 H4B 0.9141
17 GB4 0.9109
18 AZY 0.9107
19 K82 0.9083
20 DAH 0.9076
21 SJK 0.9074
22 RSV 0.9057
23 GDL 0.9037
24 4NR 0.9037
25 CIY 0.9034
26 FER 0.9033
27 4FE 0.9032
28 PMP 0.9029
29 CG 0.9026
30 NB1 0.9026
31 KF5 0.9020
32 H75 0.9013
33 5OO 0.9010
34 2FX 0.9003
35 ZEA 0.9003
36 Q0K 0.9001
37 0UL 0.8991
38 4CN 0.8982
39 3SU 0.8979
40 TRP 0.8971
41 ZSP 0.8970
42 GB5 0.8969
43 NAL 0.8969
44 2JX 0.8965
45 FMQ 0.8964
46 2WU 0.8964
47 X0T 0.8963
48 PLR 0.8961
49 5VU 0.8961
50 PIQ 0.8960
51 N7I 0.8959
52 GLP 0.8957
53 4AF 0.8957
54 FT6 0.8951
55 G6P 0.8949
56 0DF 0.8948
57 S0D 0.8944
58 PH3 0.8942
59 9NB 0.8941
60 109 0.8938
61 27K 0.8936
62 HMZ 0.8935
63 4AB 0.8935
64 KLV 0.8935
65 ALX 0.8932
66 LTM 0.8930
67 IOP 0.8925
68 LTT 0.8925
69 J1K 0.8924
70 NY4 0.8922
71 C4E 0.8919
72 MMS 0.8916
73 54E 0.8915
74 TYR 0.8915
75 GC2 0.8915
76 FCW 0.8912
77 S98 0.8911
78 3IL 0.8908
79 MQG 0.8907
80 OLU 0.8902
81 Y0V 0.8902
82 NIY 0.8896
83 96Z 0.8895
84 9H2 0.8892
85 XCG 0.8885
86 2P3 0.8884
87 ZHA 0.8883
88 BHS 0.8883
89 2GQ 0.8882
90 PXP 0.8881
91 JA5 0.8880
92 9KZ 0.8878
93 IFG 0.8877
94 OQC 0.8876
95 S0G 0.8875
96 DHC 0.8873
97 ALE 0.8870
98 NGA 0.8870
99 FYR 0.8870
100 I2E 0.8867
101 MP5 0.8866
102 1QV 0.8864
103 8NB 0.8858
104 HC4 0.8858
105 0J5 0.8857
106 SIZ 0.8851
107 K7H 0.8850
108 BNX 0.8849
109 TMG 0.8846
110 3TC 0.8845
111 QUB 0.8844
112 7AP 0.8841
113 F40 0.8841
114 FF2 0.8840
115 Q5M 0.8837
116 4R1 0.8829
117 EV2 0.8829
118 9BF 0.8827
119 92O 0.8820
120 BEU 0.8819
121 ZIP 0.8819
122 KWB 0.8818
123 SSY 0.8816
124 SYE 0.8815
125 AU8 0.8815
126 4BX 0.8814
127 BG6 0.8814
128 3LJ 0.8813
129 X48 0.8812
130 X04 0.8808
131 3VX 0.8808
132 BGU 0.8808
133 Z25 0.8807
134 CTE 0.8807
135 P4L 0.8805
136 HH6 0.8801
137 JCZ 0.8800
138 6HP 0.8799
139 0J2 0.8796
140 ZRK 0.8795
141 NEU 0.8792
142 16G 0.8790
143 2PV 0.8786
144 RK4 0.8786
145 2KU 0.8785
146 KYN 0.8783
147 2PK 0.8782
148 GJG 0.8780
149 A2G 0.8778
150 F5C 0.8774
151 8V8 0.8772
152 5M2 0.8771
153 CXH 0.8770
154 TNX 0.8768
155 363 0.8767
156 1V4 0.8765
157 4QY 0.8762
158 AMR 0.8762
159 GZV 0.8759
160 NFM 0.8758
161 1Q1 0.8758
162 L03 0.8755
163 IPO 0.8755
164 1XS 0.8754
165 78U 0.8753
166 GJK 0.8753
167 NGS 0.8748
168 HWD 0.8747
169 C9M 0.8745
170 CFA 0.8743
171 0XR 0.8741
172 5ER 0.8739
173 88R 0.8738
174 RVE 0.8738
175 CHQ 0.8734
176 BDI 0.8733
177 P81 0.8731
178 8D6 0.8725
179 K3D 0.8725
180 CC5 0.8723
181 A9K 0.8722
182 DVK 0.8721
183 4Z9 0.8720
184 SX2 0.8720
185 ZYQ 0.8717
186 2F8 0.8716
187 PW5 0.8710
188 ZYC 0.8710
189 B15 0.8709
190 5SJ 0.8708
191 80G 0.8707
192 DL6 0.8707
193 EYY 0.8707
194 PZP 0.8705
195 N91 0.8705
196 IYR 0.8704
197 EYJ 0.8699
198 9FH 0.8693
199 JPQ 0.8692
200 3L1 0.8691
201 GF4 0.8690
202 1V3 0.8688
203 E9S 0.8686
204 EE8 0.8685
205 C53 0.8684
206 7MW 0.8683
207 LO1 0.8682
208 2LT 0.8681
209 TYC 0.8673
210 D8Q 0.8670
211 H4E 0.8668
212 C0W 0.8667
213 UQ1 0.8667
214 4Z1 0.8664
215 36M 0.8658
216 ITE 0.8654
217 CDY 0.8653
218 J27 0.8652
219 6Q3 0.8649
220 A6W 0.8648
221 250 0.8645
222 BBY 0.8645
223 SNG 0.8644
224 50C 0.8643
225 RKN 0.8639
226 9VZ 0.8639
227 856 0.8636
228 WA2 0.8636
229 2CZ 0.8635
230 QIF 0.8634
231 LOG 0.8631
232 NG6 0.8628
233 5TT 0.8628
234 3D1 0.8627
235 A6P 0.8624
236 3XR 0.8621
237 86L 0.8620
238 EQW 0.8620
239 5GV 0.8620
240 52F 0.8619
241 657 0.8616
242 3W6 0.8611
243 3W3 0.8611
244 3Y7 0.8611
245 C93 0.8611
246 5WT 0.8609
247 A5P 0.8608
248 2QC 0.8603
249 RUG 0.8598
250 ALJ 0.8598
251 R4E 0.8594
252 B5A 0.8594
253 DTR 0.8593
254 MAG 0.8589
255 6PG 0.8588
256 JY2 0.8572
257 RPN 0.8572
258 AC2 0.8570
259 J38 0.8561
260 IOS 0.8559
261 1HR 0.8551
262 NPL 0.8548
263 5S9 0.8544
264 MUX 0.8540
265 A7K 0.8538
266 6N4 0.8535
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4GVF; Ligand: NDG; 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: 4gvf.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4GVF; Ligand: NAG; 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: 4gvf.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4GVF; Ligand: NAG; 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: 4gvf.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4GVF; Ligand: NDG; 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: 4gvf.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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