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Receptor
PDB id Resolution Class Description Source Keywords
4YZ5 2.27 Å EC: 3.2.1.18 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANC, IN COMPL SIALYLLACTOSE STREPTOCOCCUS PNEUMONIAE SIALIDASE NEURAMINIDASE BETA-PROPELLER CBM40 HYDROLASE
Ref.: STREPTOCOCCUS PNEUMONIAE NANC: STRUCTURAL INSIGHTS SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODU SIALIDASE INHIBITOR. J.BIOL.CHEM. V. 290 27736 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SLT A:1001;
B:801;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
Kd = 1.48 mM
633.551 C23 H39 N O19 CC(=O...
SO4 B:806;
B:803;
A:1004;
B:804;
A:1003;
A:1005;
A:1006;
B:805;
A:1007;
B:807;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
DAN A:1002;
B:802;
Valid;
Valid;
none;
none;
submit data
291.255 C11 H17 N O8 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YZ5 2.27 Å EC: 3.2.1.18 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE NANC, IN COMPL SIALYLLACTOSE STREPTOCOCCUS PNEUMONIAE SIALIDASE NEURAMINIDASE BETA-PROPELLER CBM40 HYDROLASE
Ref.: STREPTOCOCCUS PNEUMONIAE NANC: STRUCTURAL INSIGHTS SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODU SIALIDASE INHIBITOR. J.BIOL.CHEM. V. 290 27736 2015
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 4YZ2 - DAN C11 H17 N O8 CC(=O)N[C@....
2 4YW5 - G39 C14 H24 N2 O4 CCC(CC)O[C....
3 4YW2 Kd = 1.6 mM SIA GAL n/a n/a
4 5F9T - SFJ C11 H17 F2 N O8 CC(=O)N[C@....
5 4YW3 - DAN C11 H17 N O8 CC(=O)N[C@....
6 4YW1 - SIA C11 H19 N O9 CC(=O)N[C@....
7 4YZ4 - SIA C11 H19 N O9 CC(=O)N[C@....
8 4YZ5 Kd = 1.48 mM SLT C23 H39 N O19 CC(=O)N[C@....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 4YZ2 - DAN C11 H17 N O8 CC(=O)N[C@....
2 4YW5 - G39 C14 H24 N2 O4 CCC(CC)O[C....
3 4YW2 Kd = 1.6 mM SIA GAL n/a n/a
4 5F9T - SFJ C11 H17 F2 N O8 CC(=O)N[C@....
5 4YW3 - DAN C11 H17 N O8 CC(=O)N[C@....
6 4YW1 - SIA C11 H19 N O9 CC(=O)N[C@....
7 4YZ4 - SIA C11 H19 N O9 CC(=O)N[C@....
8 4YZ5 Kd = 1.48 mM SLT C23 H39 N O19 CC(=O)N[C@....
50% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 2VK6 - DAN C11 H17 N O8 CC(=O)N[C@....
2 2YA5 - SIA C11 H19 N O9 CC(=O)N[C@....
3 2JKB - SKD C11 H17 N O8 CC(=O)N[C@....
4 4FPF ic50 = 38.9 uM JKK C9 H12 Cl N O3 S c1cc(cc(c1....
5 4FOQ - TAU C2 H7 N O3 S C(CS(=O)(=....
6 4FPC - MFY C9 H12 Cl N O3 S c1cc(ccc1C....
7 4FOY - D53 C9 H13 N O3 S c1ccc(cc1)....
8 4FPL - 7HV C9 H11 Cl2 N O3 S c1cc(c(cc1....
9 4FOW - A20 C3 H9 N O3 S C(CN)CS(=O....
10 4FPJ - D8I C10 H15 N O4 S COc1cccc(c....
11 4FPK ic50 = 57.4 uM IJ1 C10 H15 N O3 S Cc1cccc(c1....
12 4FQ4 - IJ4 C10 H14 F N O3 S Cc1cc(ccc1....
13 4FPY - 0V8 C9 H12 Br N O3 S c1cc(cc(c1....
14 4X6K ic50 = 0.00487 mM 3XR C8 H15 N2 O5 CC(=O)N[C@....
15 4X47 ic50 = 1.4 mM DAN C11 H17 N O8 CC(=O)N[C@....
16 4X4A Ki = 2.37 mM SKD C11 H17 N O8 CC(=O)N[C@....
17 4YW5 - G39 C14 H24 N2 O4 CCC(CC)O[C....
18 4YW2 Kd = 1.6 mM SIA GAL n/a n/a
19 5F9T - SFJ C11 H17 F2 N O8 CC(=O)N[C@....
20 4YW3 - DAN C11 H17 N O8 CC(=O)N[C@....
21 4YW1 - SIA C11 H19 N O9 CC(=O)N[C@....
22 4YZ4 - SIA C11 H19 N O9 CC(=O)N[C@....
23 4YZ5 Kd = 1.48 mM SLT C23 H39 N O19 CC(=O)N[C@....
24 4SLI - CNP C14 H23 N O8 CC(=O)N[C@....
25 3SLI - SKD C11 H17 N O8 CC(=O)N[C@....
26 2SLI - SKD C11 H17 N O8 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SLT; Similar ligands found: 88
No: Ligand ECFP6 Tc MDL keys Tc
1 SLT 1 1
2 BGC SIA GAL 0.829787 0.98
3 SIA GAL BGC 0.829787 0.98
4 SIA GAL GLC 0.829787 0.98
5 GAL BGC SIA 0.829787 0.98
6 GLA GLC SIA 0.829787 0.98
7 BGC GAL SIA 0.829787 0.98
8 4U2 0.827957 0.960784
9 SIA SIA GLA BGC 0.722222 0.924528
10 BGC SIA SIA GAL 0.722222 0.924528
11 MN0 GAL GLC 0.705882 0.941176
12 BGC GAL SIA SIA GAL NGA 0.702703 0.942308
13 BGC GAL SIA NGA GAL SIA 0.702703 0.942308
14 4U0 0.696078 0.98
15 NAG SIA GAL 0.686275 0.942308
16 SIA SIA GAL NGA GAL 0.65812 0.924528
17 BGC GAL SIA NGA GAL 0.652174 0.942308
18 GAL NGA GAL BGC SIA 0.652174 0.942308
19 GAL NGA SIA GAL BGC 0.652174 0.942308
20 SIA GAL BGC NGA GAL 0.652174 0.942308
21 SIA GAL BGC NGA 0.637168 0.942308
22 GAL BGC SIA NGA 0.637168 0.942308
23 BGC GAL SIA NGA 0.637168 0.942308
24 SIA GAL A2G 0.628571 0.942308
25 NGA GAL SIA 0.628571 0.942308
26 NAG GAL NGC 0.627273 0.942308
27 GAL SIA NGA GAL SIA 0.621622 0.942308
28 SIA GAL NAG 0.62037 0.890909
29 BGC GAL NAG SIA GAL 0.613445 0.924528
30 SIA GAL NAG GAL GLC 0.613445 0.924528
31 SIA GAL NAG GAL BGC 0.613445 0.924528
32 SIA GAL NGS 0.596491 0.742424
33 4U1 0.581818 0.942308
34 GAL SIA 0.575758 0.98
35 SIA GAL NAG GAL 0.575221 0.924528
36 SIA GAL NAG SIA 0.573913 0.924528
37 NAG FUC SIA GAL 0.57265 0.942308
38 SIA GAL NAG FUC 0.57265 0.942308
39 SIA GAL NDG FUC 0.57265 0.942308
40 SIA GLA NAG FUC 0.57265 0.942308
41 NDG FUC SIA GAL 0.57265 0.942308
42 FUC NDG GAL SIA 0.57265 0.942308
43 SIA GAL SIA GLC NGA 0.566929 0.924528
44 SIA GAL SIA BGC NGA 0.566929 0.924528
45 GAL SIA NGA GAL 0.565217 0.942308
46 SIA GAL NGA GAL 0.565217 0.942308
47 SIA GAL NDG SIA 0.560345 0.890909
48 SIA SIA GAL NGA GAL SIA 0.556452 0.924528
49 SIA GAL MAG FUC 0.546219 0.90566
50 NAG GAL SIA 0.539823 0.924528
51 SIA GAL NGA 0.530973 0.942308
52 GAL NAG SIA GAL 0.520661 0.924528
53 SIA GLA NGS FUC 0.515625 0.742424
54 SIA 2FG 0.514286 0.907407
55 SIA NAG GAL GAL 0.512605 0.924528
56 GAL NGA GAL SIA 0.512605 0.924528
57 SIA NAG GAL 0.508621 0.890909
58 SIA 2FG NAG 0.508621 0.875
59 MNA 0.505495 0.865385
60 SIA GAL 0.504762 0.941176
61 SIA SIA GAL 0.504425 0.924528
62 SIA GAL BGC 16C 0.503597 0.790323
63 NGC GAL NGA POL AZI 0.496063 0.765625
64 NGC MBG 0.490741 0.923077
65 BGC 18C GAL SIA 0.485915 0.790323
66 BGC GAL CEQ SLB NGA GAL SIA SIA 0.479167 0.790323
67 NAG GAL BGC 0.475248 0.918367
68 LAT NAG GAL 0.471154 0.918367
69 GLC GAL NAG GAL 0.471154 0.918367
70 GAL NAG GAL GLC 0.466019 0.918367
71 BGC GAL NAG GAL 0.466019 0.918367
72 GAL TNR SIA 0.459677 0.890909
73 NGA GLA GAL BGC 0.45283 0.918367
74 GAL NGA GLA BGC GAL 0.448598 0.918367
75 SIA 0.44086 0.877551
76 SLB 0.44086 0.877551
77 MUS 0.434783 0.807018
78 SIA GAL SIA BGC NGA CEQ 0.422819 0.753846
79 NGA GAL BGC 0.421569 0.918367
80 BGC 18C GAL NGA SIA GAL 0.416149 0.790323
81 MN0 0.414141 0.865385
82 GLC NAG GAL GAL FUC 0.413793 0.9
83 FUC GAL NAG GAL BGC 0.413793 0.9
84 GAL GLC NAG GAL FUC 0.413793 0.9
85 BGC GAL NAG GAL FUC FUC 0.411765 0.92
86 GLC GAL NAG GAL FUC FUC 0.411765 0.92
87 GLA GAL GAL 0.410526 0.673469
88 NAG GAL GAL NAG GAL 0.407407 0.901961
Ligand no: 2; Ligand: DAN; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 DAN 1 1
2 9AM 0.767857 0.913043
3 4AM 0.661017 0.913043
4 ZMR 0.590909 0.792453
5 KFN 0.542373 0.704545
6 49A 0.507692 0.87234
7 0HX 0.454545 0.75
8 RP6 0.452055 0.934783
9 LNV 0.434211 0.701754
10 FSI 0.408451 0.82
11 SIA 0.4 0.911111
12 SLB 0.4 0.911111
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YZ5; Ligand: SLT; Similar sites found with APoc: 145
This union binding pocket(no: 1) in the query (biounit: 4yz5.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 6EXF LYS 1.34409
2 2DT3 NAG NAG NAG NAG NAG NAG 1.38504
3 5Y86 HRM 1.53061
4 4H6Q TFB 1.60256
5 4H6Q FAD 1.60256
6 2J7T 274 1.65563
7 2YNE YNE 1.82292
8 2YNE NHW 1.82292
9 5D4Y BXP 1.97183
10 2ZX7 ZX7 1.97802
11 1U5R ATP 2.01149
12 2ZV2 609 2.01342
13 5ZTN CUR 2.21566
14 2R5N R5P 2.24215
15 2R5N RP5 2.24215
16 4AU8 Z3R 2.36486
17 2WPU KYT 2.51572
18 4TWP AXI 2.58303
19 2WU6 DKI 2.62467
20 5JNN 6LM 2.63158
21 4G17 0VN 2.72727
22 3DLG GWE 2.72727
23 3WQV GCS GCS GCS GCS GCS 2.78481
24 2PZI AXX 2.8065
25 4X7Q 3YR 2.88462
26 2V58 LZJ 2.89532
27 6D6L FY4 2.94118
28 1ODM ASV 3.02115
29 2VRQ XYP XYP AHR 3.02419
30 1PZG A3D 3.10192
31 4YZN 4K5 3.13589
32 2WZE XYP XYP XYP 3.14815
33 2W5F XYP XYP XYP 3.14815
34 4CPH LH4 3.14961
35 5JE0 SAH 3.23887
36 5JE0 AZ8 3.23887
37 2V7O DRN 3.27381
38 3L5R 47X 3.27869
39 4LWA Q13 3.30579
40 4NKW PLO 3.39734
41 1FO3 KIF 3.47826
42 5WO4 B7V 3.64238
43 4BG4 ADP 3.65169
44 1PHK ATP 3.69128
45 1FH8 XYP XIF 3.84615
46 2VN9 GVD 3.98671
47 3C0G 3AM 3.9886
48 3W25 XYP XYP 4.16667
49 4Y0X ADP 4.26667
50 4YZC STU 4.2836
51 3AKK ADP 4.30769
52 5JM8 ATP 4.34028
53 2HY0 306 4.34783
54 2DW7 SRT 4.37018
55 3SAO NKN 4.375
56 5YF9 NIO 4.42478
57 5YBN AKG 4.4586
58 3DLS ADP 4.47761
59 4AUA 4AU 4.56026
60 3CY2 MB9 4.77707
61 2AG4 LP3 4.87805
62 2XK9 XK9 4.96894
63 3B6R ADP 4.98688
64 1WW5 SGA BGC 5
65 3E7O 35F 5
66 2X32 OTP 5.02793
67 4GGZ BTN 5.21739
68 4UX9 ANP 5.21978
69 1ZHX HC3 5.25114
70 3V8S 0HD 5.36585
71 2FGL XYS XYS XYS 5.36723
72 3AXM 6PG 5.42636
73 1SWG BTN 5.46875
74 5X8I SQZ 5.49133
75 1Y52 BTN 5.55556
76 5KLP IHP 5.55556
77 1GK8 CAP 5.71429
78 3EM0 CHD 5.7971
79 3OJI PYV 5.82011
80 1T27 PCW 5.90406
81 5BVB DOG 6.06061
82 1M15 ADP 6.16247
83 1M15 ARG 6.16247
84 2C1Q BTN 6.34921
85 3M2W L8I 6.35452
86 3ANY 2A3 6.46388
87 1ZM1 BGC BGC BGC 6.639
88 3N0Y APC 6.70391
89 3O0G 3O0 6.71141
90 2ZHL NAG GAL GAL NAG 6.75676
91 6M8N MLI 6.77966
92 6GUE FB8 6.95364
93 5VZ0 ADP 7.0901
94 4R38 RBF 7.14286
95 6EOZ 58K 7.14286
96 2Z7R STU 7.16511
97 1M6P M6P 7.23684
98 1ULE GLA GAL NAG 7.33333
99 3FAL LO2 7.43802
100 2PVF ACP 7.48503
101 4QDF 30Q 7.61421
102 3T2W BTN 8.19672
103 3SLS ANP 8.22368
104 6C7Y ADP 8.54701
105 3MHA Z69 8.86699
106 2BNJ XYP XYP AHR FER 8.91089
107 5W4W 9WG 10.2719
108 4KBA 1QM 10.2719
109 4JNJ BTN 10.4348
110 2GJ5 VD3 10.4938
111 5N87 N66 10.8626
112 1ZT1 PHE GLU ALA ASN GLY ASN LEU ILE 11
113 2BPM 529 11.3208
114 4K33 ACP 11.3846
115 4CFU 2WC 11.4504
116 4BCN T9N 11.4504
117 3JRS A8S 11.5385
118 3BU5 ATP 11.7647
119 5XNC N4P 11.8598
120 3A76 SPD 11.9318
121 6HDT BTN 12.0301
122 1V0O INR 12.1528
123 3EKK GS2 12.3779
124 5ETR 5RW 12.4224
125 5ETR APC 12.4224
126 1U0A BGC BGC BGC BGC 12.6168
127 3KFC 61X 13.0435
128 3MTX PGT 13.9073
129 2ZSC BTN 14.1844
130 3QDJ ALA ALA GLY ILE GLY ILE LEU THR VAL 15
131 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 15
132 5U98 1KX 15.1515
133 4RFR RHN 15.7635
134 5AIG VPR 16
135 4Z28 BTN 17.9104
136 4WNP 3RJ 18.1185
137 2V73 SIA 23.5602
138 1IR3 ANP 27.7778
139 1N5S ADL 28.5714
140 3E5A VX6 29.5455
141 5ZCO PGV 36.1702
142 2DYR PGV 36.1702
143 5Z84 PGV 36.1702
144 5FRE SIA GAL 43.8144
145 6ER4 SIA GAL BGC 45.8763
Pocket No.: 2; Query (leader) PDB : 4YZ5; Ligand: DAN; Similar sites found with APoc: 29
This union binding pocket(no: 2) in the query (biounit: 4yz5.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4QN7 G39 2.05128
2 3TIC ZMR 2.1322
3 4U6D 3DY 2.41546
4 3A72 AHR AHR 2.53521
5 4UDK NDG 2.59366
6 4B7J G39 2.65879
7 5EYP GTP 2.95858
8 4HZX G39 3.09278
9 3VSS FRU 3.22581
10 4N2R FUB 3.59281
11 5H7N MTT 3.76569
12 4IRL MTT 3.78151
13 2QM9 TDZ 4.51613
14 5N6N SUC 4.58333
15 4QN6 LNV 4.85933
16 3RYC GTP 4.8951
17 3E7O 35F 5
18 4AK7 47N 5.44554
19 4LNU GTP 5.91716
20 4BVM VCA 6.01504
21 4BVM PLM 6.01504
22 5B2D SLT 7.15746
23 5LXT GTP 8.59375
24 2DHC DCE 9.35484
25 5GOP FRU 9.97831
26 5GOO FRU 9.97831
27 5ITZ GTP 10.0775
28 5M1Z 6LW AHR 14.1689
29 2V2V V12 18.0812
Pocket No.: 3; Query (leader) PDB : 4YZ5; Ligand: SLT; Similar sites found with APoc: 21
This union binding pocket(no: 3) in the query (biounit: 4yz5.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 3FU7 D2M 1.78891
2 5HES 032 1.9544
3 1VA6 ADP 2.3166
4 1X9D SMD 2.97398
5 4PLT OXM 3.02115
6 3HZT J60 3.10192
7 4IX4 ADP 3.14286
8 4F4P 0SB 3.2967
9 4YMJ 4EJ 4.27632
10 4GAA BES 4.5977
11 4O9S 2RY 5.11628
12 6CEN ACE GLY VAL NLE ARG ILE NH2 5.70175
13 2V63 CAP 5.71429
14 1ERB ETR 6.01093
15 3STK PLM 6.06061
16 4QAC KK3 7.8341
17 1WMA AB3 7.97101
18 1WMA NDP 7.97101
19 5IXG OTP 8.87574
20 4BJ8 BTN 10.3175
21 5LXM ADP 28.9474
Pocket No.: 4; Query (leader) PDB : 4YZ5; Ligand: DAN; Similar sites found with APoc: 4
This union binding pocket(no: 4) in the query (biounit: 4yz5.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2IOY RIP 5.30035
2 6F1J EDG 7.38462
3 2BTO GTP 8.33333
4 3HST MLR 9.92908
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