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Receptor
PDB id Resolution Class Description Source Keywords
5KD8 2.3 Å EC: 7.-.-.- BT_4244 METALLOPEPTIDASE IN COMPLEX WITH TN ANTIGEN. BACTEROIDES THETAIOTAOMICRON (STRAIN A/ DSM 2079 / NCTC 10582 / E50 / VPI-5482) O-GLYCOPEPTIDASE PF13402/M60-LIKE O-GLYCAN HYDROLASE. HY
Ref.: RECOGNITION OF PROTEIN-LINKED GLYCANS AS A DETERMIN PEPTIDASE ACTIVITY. PROC. NATL. ACAD. SCI. V. 114 E679 2017 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA A:906;
A:905;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
NI A:904;
A:903;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
TNR A:902;
Valid;
none;
submit data
308.285 C11 H20 N2 O8 CC(=O...
ZN A:901;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KD8 2.3 Å EC: 7.-.-.- BT_4244 METALLOPEPTIDASE IN COMPLEX WITH TN ANTIGEN. BACTEROIDES THETAIOTAOMICRON (STRAIN A/ DSM 2079 / NCTC 10582 / E50 / VPI-5482) O-GLYCOPEPTIDASE PF13402/M60-LIKE O-GLYCAN HYDROLASE. HY
Ref.: RECOGNITION OF PROTEIN-LINKED GLYCANS AS A DETERMIN PEPTIDASE ACTIVITY. PROC. NATL. ACAD. SCI. V. 114 E679 2017 U.S.A.
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 5KD8 - TNR C11 H20 N2 O8 CC(=O)N[C@....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5KD8 - TNR C11 H20 N2 O8 CC(=O)N[C@....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 5KD8 - TNR C11 H20 N2 O8 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TNR; Similar ligands found: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 TNR 1 1
2 3YW 0.683333 0.895833
3 MAG 0.559322 0.84
4 2F8 0.559322 0.84
5 NG1 0.548387 0.741379
6 GN1 0.548387 0.741379
7 ACA SER SER VAL GLY A2G 0.5 0.90566
8 ACE SER SER VAL GLY A2G 0.5 0.886792
9 NAG GAL 0.485714 0.86
10 GAL NAG 0.485714 0.86
11 NAG NGA 0.478873 0.882353
12 NAG A2G 0.478873 0.882353
13 NAG MBG 0.478873 0.826923
14 NAG A2G GAL 0.475 0.882353
15 A2G MBG 0.472222 0.826923
16 MBG A2G 0.472222 0.826923
17 NAG MAN 0.465753 0.862745
18 GYU 0.464789 0.854545
19 57S 0.461538 0.762712
20 NAG GDL 0.458333 0.882353
21 CBS CBS 0.458333 0.882353
22 NDG NAG 0.458333 0.882353
23 CBS 0.458333 0.882353
24 NAG NM9 0.45 0.867925
25 HD4 0.448718 0.762712
26 MA8 0.445946 0.901961
27 NGA GAL 0.445946 0.843137
28 GAL NGA A2G 0.441558 0.882353
29 NAG NAG NAG NAG NDG 0.434211 0.865385
30 NAG NAG NAG NAG NAG 0.434211 0.865385
31 NAG NAG NDG NAG 0.434211 0.865385
32 NAG NAG NAG NAG NAG NAG 0.434211 0.865385
33 NAG NAG NAG NDG 0.434211 0.865385
34 CTO 0.434211 0.865385
35 NAG NAG NDG 0.434211 0.865385
36 NAG NAG NAG NAG NAG NAG NAG NAG 0.434211 0.865385
37 NDG NAG NAG NDG 0.434211 0.865385
38 NDG NAG NAG NAG 0.434211 0.865385
39 NAG NAG 0.434211 0.867925
40 NAG NDG 0.434211 0.867925
41 NDG NAG NAG 0.434211 0.865385
42 NAG MAN BMA 0.43038 0.86
43 LEC 0.428571 0.676923
44 6ZC 0.428571 0.676923
45 NGA 0.42623 0.833333
46 BM3 0.42623 0.833333
47 HSQ 0.42623 0.833333
48 A2G 0.42623 0.833333
49 NDG 0.42623 0.833333
50 NAG 0.42623 0.833333
51 NGA SER GAL 0.425 0.941176
52 NAG MAN MMA 0.425 0.826923
53 A2G SER GAL 0.425 0.941176
54 GAL TNR 0.425 0.941176
55 GAL SER A2G 0.425 0.941176
56 NAG MUB 0.421687 0.849057
57 NAG AMU 0.421687 0.849057
58 A2G GLA FUC 0.419753 0.843137
59 FUC GLA A2G 0.419753 0.843137
60 FUC GAL A2G 0.419753 0.843137
61 A2G GAL FUC 0.419753 0.843137
62 NGA GAL FUC 0.419753 0.843137
63 3QL 0.417722 0.818182
64 GYT 0.417722 0.783333
65 NGA GAL BGC 0.417722 0.86
66 DLD 0.416667 0.766667
67 SNG 0.415385 0.769231
68 NAG MAN MAN 0.409639 0.86
69 THR NGA GAL NAG 0.408602 0.867925
70 AH0 NAG 0.404762 0.789474
71 NAG AMU NAG AMV 0.4 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KD8; Ligand: TNR; Similar sites found with APoc: 239
This union binding pocket(no: 1) in the query (biounit: 5kd8.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 5IKH 6BW 0.909091
3 2VJ8 HA2 1.25224
4 3LXI CAM 1.42518
5 4BXK 1IU 1.61002
6 4CA5 3EF 1.61002
7 5AMC GLY NIY 1.61002
8 3H78 BE2 1.67131
9 2OBD PCW 1.68067
10 5O7E 9NB 1.78117
11 3X01 AMP 1.78117
12 5HTX ADP 1.82232
13 3C88 ARG ARG GLY CYS NH2 1.85185
14 3Q8G PEE 1.875
15 5OHJ 9VE 1.90024
16 2J83 BAT 1.9084
17 2FV5 541 1.91571
18 4OKZ 3E9 1.91781
19 5G57 6M5 1.94444
20 4GAA BES 1.9678
21 2W41 ADP 1.97239
22 4JD3 COA 1.983
23 4JD3 PLM 1.983
24 2Z7I 742 2.05882
25 5B0W 22B 2.06186
26 3QCP FAD 2.12766
27 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 2.14669
28 3G4G D71 2.14669
29 1P1M MET 2.21675
30 2XXP DSL 2.26131
31 3GWT 066 2.26629
32 3O01 DXC 2.27273
33 1YQZ FAD 2.28311
34 4LRL TTP 2.29167
35 4LRL DGT 2.29167
36 3T58 FAD 2.31214
37 3SDV 911 2.32558
38 3V66 D3A 2.35294
39 4XU6 TDA 2.38095
40 2BCG GER 2.42718
41 3E3U NVC 2.53807
42 4RHP PEF 2.55319
43 4QHP 32Q 2.68336
44 4LY9 1YY 2.68336
45 4LY9 S6P 2.68336
46 3NHT U46 2.7027
47 3G5K BB2 2.73224
48 6F8B CXH 2.86225
49 3ZOK GLY 2.91005
50 1ATL 0QI 2.9703
51 3DZT EAH 2.9703
52 6BTN E8M 2.9703
53 5AHO TLA 2.97619
54 4AIG FLX 2.98507
55 3LLI FAD 3.06513
56 1TMX HGX 3.07167
57 1SR7 MOF 3.0888
58 1ZED PNP 3.09917
59 1D6H COA 3.10078
60 4OAR 2S0 3.10078
61 4WZV E40 3.125
62 4F0B GDS 3.125
63 1K7L 544 3.125
64 5V13 JH3 3.125
65 1BUC CAA 3.13316
66 3WYJ H78 3.16206
67 4M0R 644 3.16623
68 2YB9 HA0 3.22004
69 3DWB RDF 3.22004
70 3G9E RO7 3.22004
71 2E2R 2OH 3.27869
72 6C1R EFD 3.31754
73 5W8Q BU4 3.33333
74 4L1F COS 3.39426
75 5W7D PX8 3.39893
76 4KX8 L2O VAL VAL ASP 3.39893
77 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.40136
78 1MV8 NAD 3.44037
79 3PVT 3HC 3.4749
80 4U0S ADP 3.48837
81 5N5U 7N8 3.50318
82 3EWC MCF 3.50404
83 6BMS POV 3.51906
84 2RHW C0E 3.53357
85 2TCL RO4 3.5503
86 4JE7 BB2 3.5533
87 4JZX 476 3.59116
88 4DR9 BB2 3.64583
89 1Q1Y BB2 3.66492
90 4KBS PX2 3.72093
91 1HFS L04 3.75
92 3ZVS MLI 3.75
93 2OKL BB2 3.78378
94 5F1R 42O 3.79747
95 4DV8 0LX 3.80228
96 1DKF BMS 3.86266
97 5JE8 NAD 3.97351
98 6CIB ADP 3.97878
99 5UGW GSH 4
100 6GL8 F3Q 4.06977
101 2A1L PCW 4.07407
102 1QV1 CZH 4.10256
103 1G27 BB1 4.16667
104 1UHK CZN 4.18848
105 3QCJ NX4 4.19355
106 4IN9 SER TRP PHE PRO 4.21687
107 5LOF 70R 4.2471
108 4WKI 3PW 4.25532
109 2UXI G50 4.28571
110 5V4R MGT 4.32099
111 1LQY BB2 4.34783
112 1RQJ RIS 4.34783
113 2ALG DAO 4.34783
114 2ALG HP6 4.34783
115 5M37 9SZ 4.34783
116 2X34 UQ8 4.41989
117 4LPG 1MV 4.53333
118 1FBL HTA 4.59459
119 1JF0 CZH 4.61538
120 2YPO PHE 4.7619
121 4DOE CBK 4.84211
122 5NI5 8YB 4.86111
123 2BIF BOG 4.90405
124 5K52 OCD 4.90566
125 4PGK Y69 4.91803
126 5LX9 OLB 4.92958
127 5K53 STE 4.96183
128 5W7B PA1 PO4 FTT FTT GCS FTT PO4 KDO MYR 4.96454
129 5W7B MYR 4.96454
130 4DXJ 0M9 4.97238
131 5IF4 6AK 5.03145
132 5X5M 7YU 5.09259
133 5MTE BB2 5.10949
134 3VSV XYP 5.17241
135 2ZXG S23 5.18784
136 5FPN KYD 5.18784
137 6ESN BWE 5.24345
138 4B52 RDF 5.26316
139 4ZB6 GDS 5.38117
140 3Q2H QHF 5.38721
141 5NTW 98N 5.44747
142 4DOL PLM 5.52995
143 2J8C SPO 5.53746
144 2J8C U10 5.53746
145 1S17 GNR 5.55556
146 5AAV GW5 5.55556
147 4BNU 9KQ 5.57621
148 3D04 SAK 5.66038
149 4COL DTP 5.72451
150 2F1K NAP 5.73477
151 1JQ9 PHE LEU SER TYR LYS 5.78512
152 2P1C GG3 5.89744
153 2Q0D ATP 5.94901
154 4JHG ZEA 5.95238
155 4TMN 0PK 6.01266
156 1XON PIL 6.01719
157 1XM4 PIL 6.03015
158 5UR6 8KM 6.07735
159 1PZO CBT 6.08365
160 3KRO DST 6.1017
161 3KRO IPE 6.1017
162 3B1F NAD 6.2069
163 4Q86 AMP 6.44007
164 3ZCB ATP 6.45161
165 5LWY OLA 6.54206
166 3QKD HI0 6.62983
167 3GGO NAI 6.6879
168 3GGO ENO 6.6879
169 3WCA FPS 6.84932
170 3N7S 3N7 6.95652
171 3D3X ARG ILE MET GLU NH2 7.02576
172 5KAU RHQ 7.27273
173 1Q3A NGH 7.27273
174 5UWA 8ND 7.38916
175 3KMZ EQO 7.5188
176 5TVI O8N 7.6087
177 1XVB BHL 7.64706
178 5DUF G7A 7.98479
179 3KPX CZH 8.08081
180 4LWU 20U 8.23529
181 2BJ4 OHT 8.33333
182 6FS0 E4W 8.37209
183 2FP2 TSA 8.43373
184 4S1B 2BA 8.55856
185 1ZVX FIN 8.58896
186 3KP6 SAL 8.60927
187 6BA2 7KM 8.81356
188 1KUK PCA LYS TRP 8.86699
189 1WS1 BB2 8.97436
190 1YUC EPH 9.01961
191 3GKJ HC3 9.05172
192 2PSM BAM 9.09091
193 3ET1 ET1 9.27835
194 3WV1 WHH 9.35672
195 4CPH LH4 9.44882
196 2G5C NAD 9.60854
197 4YSX E23 9.61539
198 3QUZ QUV 9.95851
199 4OGQ SQD 10.0559
200 4OGQ 7PH 10.0559
201 1I0B PEL 10.241
202 4GFD 0YB 10.2439
203 3Q3C NAD 10.3679
204 3TGE TGE 10.4294
205 5M36 9SZ 10.5263
206 2VG1 FPP 10.5263
207 5GVH FMN 10.828
208 4ZW3 4S9 10.9123
209 1R6N 434 11.3744
210 2VWA PTY 11.8812
211 5G5W R8C 12.5
212 5OM2 DXT 12.5
213 5FVJ ACO 13.253
214 3AQT RCO 13.4694
215 1MMQ RRS 13.5294
216 3T6E UQ9 13.9535
217 3T6E MQ9 13.9535
218 1T27 PCW 14.0221
219 1NU4 MLA 14.433
220 2FKW RG1 16.9811
221 4V1T ADP 17.1875
222 5W97 CHD 17.6471
223 5Z84 CHD 17.6471
224 5ZCO CHD 17.6471
225 5JF2 SF7 17.6471
226 5ZCO PEK 17.6471
227 2DYS PGV 17.6471
228 5ZCO PGV 17.6471
229 5Z84 TGL 17.6471
230 5ZCO PSC 17.6471
231 5ZCO TGL 17.6471
232 4EOX 0S5 17.734
233 4ZGM 32M 19.3548
234 2Y69 CHD 21.25
235 4MNS 2AX 23.2704
236 4HBM 0Y7 24.1667
237 4OAS 2SW 30.2083
238 1RV1 IMZ 34.1176
239 5KDS A2G THR ALA PRO GLY GLY NAG SIA 43.7736
240 1UO4 PIH 50
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