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Receptor
PDB id Resolution Class Description Source Keywords
1PNF 2 Å EC: 3.5.1.52 PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE ELIZABETHKINGIA MENINGOSEPTICA HYDROLASE
Ref.: ACTIVE SITE AND OLIGOSACCHARIDE RECOGNITION RESIDUE PEPTIDE-N4-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE F. J.BIOL.CHEM. V. 270 29493 1995
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NDG NAG A:431;
Valid;
none;
submit data
424.403 n/a O=C(N...
SO4 A:500;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1PNF 2 Å EC: 3.5.1.52 PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE ELIZABETHKINGIA MENINGOSEPTICA HYDROLASE
Ref.: ACTIVE SITE AND OLIGOSACCHARIDE RECOGNITION RESIDUE PEPTIDE-N4-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE F. J.BIOL.CHEM. V. 270 29493 1995
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1PNF - NDG NAG n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1PNF - NDG NAG n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1PNF - NDG NAG n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDG NAG; Similar ligands found: 200
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG GDL 1 1
2 NDG NAG 1 1
3 CBS 1 1
4 CBS CBS 1 1
5 NAG NAG NAG NAG NAG NAG 0.929825 0.979592
6 NAG NAG NDG NAG 0.929825 0.979592
7 NAG NAG NAG NDG 0.929825 0.979592
8 NAG NAG NAG NAG NDG 0.929825 0.979592
9 NAG NAG NAG NAG NAG NAG NAG NAG 0.929825 0.979592
10 NAG NAG NDG 0.929825 0.979592
11 NDG NAG NAG NDG 0.929825 0.979592
12 NDG NAG NAG NAG 0.929825 0.979592
13 NDG NAG NAG 0.929825 0.979592
14 CTO 0.929825 0.979592
15 NAG NAG NAG NAG NAG 0.929825 0.979592
16 NAG GAL NAG 0.8 1
17 SN5 SN5 0.725806 0.826923
18 NDG GAL 0.716667 0.9375
19 GAL NDG 0.716667 0.9375
20 NLC 0.716667 0.9375
21 TCG 0.685714 0.827586
22 A2G GAL NAG FUC 0.675325 0.979592
23 FUC GAL NAG A2G 0.675325 0.979592
24 NGA GAL BGC 0.661765 0.9375
25 NAG A2G 0.65625 1
26 NAG NGA 0.65625 1
27 A2G MBG 0.646154 0.938776
28 MBG A2G 0.646154 0.938776
29 GAL NAG GAL NAG GAL NAG 0.643836 0.979592
30 NAG GAL GAL NAG 0.643836 1
31 NAG GAL 0.640625 0.9375
32 GAL NAG 0.640625 0.9375
33 NAG NAG NAG NAG 0.625 0.90566
34 NAG NAG NAG 0.625 0.90566
35 GLA GAL NAG 0.623188 0.9375
36 MAN BMA NAG 0.623188 0.9375
37 NAG NAG 0.617647 0.903846
38 NAG NDG 0.617647 0.903846
39 NAG FUC 0.615385 0.916667
40 NAG BMA NAG MAN MAN NAG NAG 0.609195 0.979592
41 NAG GAL BGC 0.60274 0.9375
42 FUC GAL NDG 0.597222 0.958333
43 NAG GAL FUC 0.597222 0.958333
44 DR2 0.597222 0.958333
45 FUC GAL NAG 0.597222 0.958333
46 FUL GAL NAG 0.597222 0.958333
47 NDG GAL FUC 0.597222 0.958333
48 GAL NAG FUC 0.597222 0.958333
49 NGA GAL 0.588235 0.88
50 NAG MUB 0.586667 0.96
51 NAG AMU 0.586667 0.96
52 NAG MAN BMA 0.583333 0.9375
53 NAG MBG 0.58209 0.938776
54 DLD 0.578947 0.827586
55 GAL NGA A2G 0.577465 1
56 NAG NAG BMA MAN MAN NAG GAL NAG 0.576087 0.979592
57 G6S NAG 0.575342 0.71875
58 NOJ NAG NAG 0.571429 0.872727
59 NOJ NAG NAG NAG 0.571429 0.857143
60 Z4S NAG NAG 0.571429 0.90566
61 NAG MAN BMA NDG MAN NAG GAL 0.565217 0.979592
62 NAG NAG BMA MAN MAN 0.564706 1
63 NGA GLA GAL BGC 0.564103 0.9375
64 M5G 0.55914 1
65 NAG MAN MAN 0.552632 0.9375
66 NGT NAG 0.552632 0.79661
67 MAG 0.55 0.877551
68 NAG NAG NGT 0.55 0.813559
69 6Y2 0.55 0.75
70 2F8 0.55 0.877551
71 3QL 0.547945 0.923077
72 NGA GAL FUC 0.546667 0.958333
73 FUC GLA A2G 0.546667 0.958333
74 A2G GLA FUC 0.546667 0.958333
75 FUC GAL A2G 0.546667 0.958333
76 A2G GAL FUC 0.546667 0.958333
77 HSQ 0.54386 0.833333
78 NAG 0.54386 0.833333
79 A2G 0.54386 0.833333
80 NGA 0.54386 0.833333
81 NDG 0.54386 0.833333
82 BM3 0.54386 0.833333
83 NAG MAN 0.542857 0.938776
84 HS2 0.540541 0.862745
85 GAL NAG MAN 0.540541 0.9375
86 MAN MAN NAG 0.539474 0.9
87 NAG MAN MMA 0.533333 0.938776
88 KPM 0.53012 0.903846
89 NAG AMU NAG AMV 0.53012 0.941176
90 UNU GAL NAG 0.525 0.94
91 NAG MAN MAN MAN NAG 0.52439 1
92 NAG NM9 0.519481 0.941176
93 A2G GAL BGC FUC 0.517647 0.958333
94 NG1 0.515625 0.741379
95 GN1 0.515625 0.741379
96 GAL BGC NAG GAL 0.512821 0.9375
97 LAT NAG GAL 0.5125 0.9375
98 GLC GAL NAG GAL 0.5125 0.9375
99 BMA Z4Y NAG 0.512195 0.918367
100 NAA NAA AMI 0.511628 0.738462
101 AO3 0.511628 0.738462
102 NAG MAN MAN MAN NAG GAL NAG GAL 0.51087 0.979592
103 MAN BMA NAG NAG MAN NAG GAL GAL 0.51087 0.979592
104 ASG 0.507692 0.65625
105 AH0 NAG 0.506329 0.888889
106 NAG NAG BMA 0.506329 0.923077
107 NAG NDG BMA 0.506329 0.923077
108 GCS GCS NAG 0.506173 0.901961
109 NAG GAL FUC FUC A2G 0.505747 0.979592
110 FUC GAL NAG A2G FUC 0.505747 0.979592
111 NAG GAL GAL NAG GAL 0.5 1
112 GUM 0.5 0.857143
113 NAG BMA MAN MAN MAN MAN 0.494253 0.9375
114 FUC BGC GAL NAG 0.494118 0.958333
115 GAL NAG GAL 0.493671 0.9
116 8VZ 0.492754 0.979592
117 UMG 0.488889 0.857143
118 BGC FUC GAL FUC A2G 0.488372 0.938776
119 NAG BDP NAG BDP NAG BDP NAG 0.488372 0.96
120 GLC FUC GAL FUC A2G 0.488372 0.938776
121 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.484848 1
122 NAG MAN BMA MAN NAG GAL 0.483871 1
123 GYU 0.478873 0.821429
124 3YW 0.478261 0.857143
125 MMA MAN NAG MAN NAG NAG 0.476744 0.96
126 NAG NAG BMA MAN NAG 0.473684 0.90566
127 BEK GAL NAG 0.47191 0.842105
128 GAL NGA 0.471429 0.9375
129 A2G GAL 0.471429 0.9375
130 GAL A2G 0.471429 0.9375
131 NAG A2G GAL 0.469136 1
132 NAG GCU NAG GCD 0.463918 0.888889
133 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.462366 0.9375
134 MA8 0.459459 0.830189
135 GAL NAG GAL BGC 0.458824 0.9
136 NAG AH0 0.458824 0.888889
137 LEC NGA 0.458824 0.75
138 TNR 0.458333 0.882353
139 NAG NAG BMA MAN 0.454545 0.923077
140 NAG AMU ALA DGL 0.453608 0.888889
141 JXD 0.453608 0.705882
142 GAL NAG GAL GLC 0.451219 0.9375
143 BGC GAL NAG GAL 0.451219 0.9375
144 A2G GAL NAG FUC GAL GLC 0.44898 0.979592
145 GLC GAL NAG GAL FUC A2G 0.44898 0.979592
146 NAG MU2 0.44898 0.872727
147 BGA 0.444444 0.807018
148 FHY 0.443182 0.90566
149 GAL NDG FUC 0.443038 0.958333
150 FUC NDG GAL 0.443038 0.958333
151 NAG NAG BMA BMA 0.44186 0.888889
152 NAG NAG BMA MAN MAN NAG NAG 0.441176 0.90566
153 GAL NAG FUC FUC 0.439024 0.938776
154 FUC GAL NDG FUC 0.439024 0.938776
155 BCW 0.439024 0.938776
156 FUC NAG GAL FUC 0.439024 0.938776
157 BDZ 0.439024 0.938776
158 FUC GAL NAG FUC 0.439024 0.938776
159 FUC NDG GAL FUC 0.439024 0.938776
160 GAL NDG FUC FUC 0.439024 0.938776
161 3PV 0.438202 0.884615
162 WZ5 0.434783 0.938776
163 NAG GDL PHJ 0.431579 0.786885
164 SNG 0.430769 0.803922
165 GYT 0.43038 0.813559
166 GAL NGA GLA BGC GAL 0.430233 0.9375
167 FUC BGC GAL NAG GAL 0.430108 0.958333
168 NDG BDP BDP NPO NDG 0.43 0.75
169 NA1 NAA AMI 0.427083 0.727273
170 SN5 SN5 NGT 0.425287 0.716667
171 SIA GAL NGA 0.424242 0.923077
172 6ZC 0.423077 0.703125
173 LEC 0.423077 0.703125
174 4U2 0.42268 0.941176
175 SN5 NGT 0.421687 0.716667
176 4U1 0.42 0.923077
177 NAG GAL SIA 0.42 0.90566
178 FUC C4W NAG BMA MAN NAG 0.415094 0.923077
179 FUC C4W NAG BMA 0.414894 0.923077
180 DR3 0.414634 0.958333
181 NAG SIA GAL 0.414141 0.923077
182 NAG GAL NGC 0.413462 0.886792
183 NAG BMA 0.413333 0.846154
184 4QY 0.411765 0.724138
185 16G 0.411765 0.724138
186 BMX 0.411765 0.724138
187 YX1 0.411765 0.646154
188 GAL MGC 0.410959 0.938776
189 ACE SER SER VAL GLY A2G 0.409091 0.851852
190 ACA SER SER VAL GLY A2G 0.409091 0.836364
191 HD4 0.407407 0.733333
192 STZ 0.405797 0.671875
193 GLC NAG GAL GAL FUC 0.404255 0.958333
194 FUC GAL NAG GAL BGC 0.404255 0.958333
195 GAL GLC NAG GAL FUC 0.404255 0.958333
196 BGC GAL SIA NGA 0.40367 0.923077
197 SIA GAL BGC NGA 0.40367 0.923077
198 GAL BGC SIA NGA 0.40367 0.923077
199 57S 0.402439 0.733333
200 ALA NAG AH0 DAL 0.402062 0.872727
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1PNF; Ligand: NDG NAG; Similar sites found with APoc: 100
This union binding pocket(no: 1) in the query (biounit: 1pnf.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1G27 BB1 None
2 5DJT FMN None
3 3PPQ CHT 1.28617
4 1NE7 16G 1.38408
5 1SJD NPG 1.59236
6 3OYZ ACO 1.91083
7 2R42 FPS 1.91083
8 5NJI 8Z2 1.91083
9 5XNC N4P 1.91083
10 3MCT 3MC 2.0202
11 5SVV FMN 2.18978
12 2OM2 GDP 2.54777
13 1QMG APX 2.54777
14 4GU5 FAD 2.54777
15 4TSK NDP 2.54777
16 1SR7 MOF 2.7027
17 1WK9 TSB 2.73973
18 1B8O IMH 2.8169
19 4CFP NAG AMU NAG AMV 2.86624
20 4RKC PMP 2.86624
21 1ZM1 BGC BGC BGC 2.90456
22 5DRB 5FJ 3.09278
23 2ZC0 PMP 3.18471
24 5AA4 6X4 3.18471
25 3V4S ATP 3.18471
26 3LJU IP9 3.18471
27 4OEV OXL 3.18471
28 4FJU GLV 3.50318
29 4FJU NAI 3.50318
30 5UBG PRT 3.53982
31 1I0S NAP 3.5503
32 4G6I RS3 3.80952
33 2Z6C FMN 3.87597
34 2V54 TYD 3.92157
35 5K13 6Q7 4.06504
36 2JDC CAO 4.10959
37 4A2A ATP 4.14013
38 5XWV 8H6 4.14013
39 4QIJ 1HA 4.14013
40 4A2B AGS 4.14013
41 2FY3 CHT 4.14013
42 1DJN FMN 4.14013
43 2VL8 UDP 4.14013
44 2VL8 CTS 4.14013
45 3M6P BB2 4.14508
46 4HBM 0Y7 4.16667
47 1DKF BMS 4.25532
48 2EW5 Y12 4.41989
49 1KQB BEZ 4.60829
50 1KQB FMN 4.60829
51 3PPM JG1 4.77707
52 4RHE FMN 4.78469
53 1L1Q 9DA 4.83871
54 1S17 GNR 5
55 2CWH NDP 5.09554
56 2CWH PYC 5.09554
57 5LYR MAN MNM 5.09554
58 3FAL LO2 5.09554
59 3KFC 61X 5.13834
60 3KP6 SAL 5.29801
61 1M5B BN1 5.32319
62 2Z6D FMN 5.38462
63 2WDB NAG MAN 5.41401
64 3R1V AZB 5.51181
65 5AGR A52 5.60345
66 4R38 RBF 5.71429
67 4GQB 0XU 5.73248
68 5FA5 MTA 5.73248
69 3HRD FAD 5.74324
70 2GJ3 FAD 5.83333
71 6GG9 FMN 6.17284
72 6BN0 NAG NAG NAG NAG NAG NAG 6.32911
73 2P8U COA 6.36943
74 1N9L FMN 6.42202
75 3D72 FAD 6.71141
76 1KUV CA5 6.76329
77 4KOT CE3 6.79012
78 1ICV FMN 6.91244
79 4WNK 453 7.00637
80 2V0C ANZ 7.32484
81 4R5Z SIN 7.62943
82 4R5Z PMP 7.62943
83 3PVW QRX 7.64331
84 4RYV ZEA 7.74194
85 5ZGI SIN 7.85124
86 1RM0 D6P 7.96178
87 1WK8 VMS 8.24742
88 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 8.42105
89 4YBN FAD 8.92857
90 4ZOH FAD 8.99281
91 1N62 FAD 9.03614
92 1XVB BHL 9.23567
93 3RMK BML 9.63855
94 1Z2I NAD 9.87261
95 4USQ FAD 10.1911
96 3R5J ACE ALA ASP VAL ALA ASA 11.6071
97 1U0A BGC BGC BGC BGC 12.6168
98 5H20 GLC 13.5135
99 3T50 FMN 17.1875
100 4INW 1EY 22.1429
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