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Receptor
PDB id Resolution Class Description Source Keywords
4DYG 1.7 Å EC: 3.2.1.14 CRYSTAL STRUCTURE OF A FAMILY GH-19 CHITINASE FROM RYE SEEDS COMPLEX WITH (GLCNAC)4 SECALE CEREALE CHITINASE HYDROLASE CARBOHYDRATE
Ref.: CRYSTAL STRUCTURE AND CHITIN OLIGOSACCHARIDE-BINDIN A 'LOOPFUL' FAMILY GH19 CHITINASE FROM RYE, SECALE SEEDS FEBS J. V. 279 3639 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MES A:305;
B:305;
Valid;
Valid;
none;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
NAG NAG NAG NAG A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
814.792 n/a O=C(N...
SO4 A:306;
A:307;
B:306;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
ZN A:308;
A:309;
A:310;
A:311;
B:307;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DYG 1.7 Å EC: 3.2.1.14 CRYSTAL STRUCTURE OF A FAMILY GH-19 CHITINASE FROM RYE SEEDS COMPLEX WITH (GLCNAC)4 SECALE CEREALE CHITINASE HYDROLASE CARBOHYDRATE
Ref.: CRYSTAL STRUCTURE AND CHITIN OLIGOSACCHARIDE-BINDIN A 'LOOPFUL' FAMILY GH19 CHITINASE FROM RYE, SECALE SEEDS FEBS J. V. 279 3639 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 4J0L - NAG NAG NAG NAG n/a n/a
2 4DYG - NAG NAG NAG NAG n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 3CQL Ka = 4 M^-1 NAG C8 H15 N O6 CC(=O)N[C@....
2 4J0L - NAG NAG NAG NAG n/a n/a
3 4DYG - NAG NAG NAG NAG n/a n/a
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 3WH1 - NAG NAG NAG NAG n/a n/a
2 4IJ4 - NAG NAG NAG NAG n/a n/a
3 3CQL Ka = 4 M^-1 NAG C8 H15 N O6 CC(=O)N[C@....
4 4J0L - NAG NAG NAG NAG n/a n/a
5 4DYG - NAG NAG NAG NAG n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MES; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 MES 1 1
Ligand no: 2; Ligand: NAG NAG NAG NAG; Similar ligands found: 126
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG NAG NAG 1 1
2 NAG NAG NAG NAG 1 1
3 NAG NAG 0.890625 0.962264
4 NAG NDG 0.890625 0.962264
5 NAG NAG BMA 0.830986 0.981132
6 NAG NDG BMA 0.830986 0.981132
7 NAG NAG BMA MAN 0.7375 0.981132
8 NAG NAG BMA MAN NAG 0.735632 1
9 NAG NAG BMA BMA 0.730769 0.981481
10 NAG NAG BMA MAN MAN NAG NAG 0.680851 1
11 NAG NAG NAG NDG 0.680556 0.924528
12 NAG NAG NAG NAG NAG 0.680556 0.924528
13 NDG NAG NAG NDG 0.680556 0.924528
14 NAG NAG NDG 0.680556 0.924528
15 NAG NAG NAG NAG NDG 0.680556 0.924528
16 NAG NAG NAG NAG NAG NAG NAG NAG 0.680556 0.924528
17 NAG NAG NDG NAG 0.680556 0.924528
18 CTO 0.680556 0.924528
19 NAG NAG NAG NAG NAG NAG 0.680556 0.924528
20 NDG NAG NAG NAG 0.680556 0.924528
21 NDG NAG NAG 0.680556 0.924528
22 NAG BMA 0.647887 0.90566
23 NOJ NAG NAG 0.62963 0.894737
24 NOJ NAG NAG NAG 0.62963 0.912281
25 Z4S NAG NAG 0.62963 0.859649
26 NDG NAG 0.625 0.90566
27 CBS CBS 0.625 0.90566
28 CBS 0.625 0.90566
29 NAG GDL 0.625 0.90566
30 NAG NAG BMA MAN MAN MAN MAN 0.584158 0.981132
31 A2G MBG 0.573333 0.851852
32 MBG A2G 0.573333 0.851852
33 NGA GAL 0.565789 0.867925
34 GAL NAG GAL 0.554217 0.886792
35 NAG NAG NGT 0.551724 0.777778
36 GAL NAG GAL BGC 0.551724 0.886792
37 NGA GAL BGC 0.55 0.849057
38 GAL NAG 0.546667 0.849057
39 NAG GAL 0.546667 0.849057
40 DLD 0.541176 0.790323
41 NAG AMU NAG AMV 0.533333 0.890909
42 3QL 0.530864 0.842105
43 GAL NAG MAN 0.52439 0.849057
44 NAG GAL NAG 0.52381 0.90566
45 MAN MAN NAG 0.52381 0.886792
46 NAG A2G 0.519481 0.90566
47 NAG NGA 0.519481 0.90566
48 TCG 0.517647 0.790323
49 6Y2 0.516854 0.720588
50 AO3 0.516129 0.710145
51 NAA NAA AMI 0.516129 0.710145
52 NAG MAN BMA 0.506024 0.849057
53 NAG GAL GAL NAG GAL 0.505747 0.90566
54 NAG MBG 0.5 0.851852
55 GAL NGA A2G 0.5 0.90566
56 NAG NAG FUL BMA MAN MAN NAG GAL 0.495495 1
57 UMG 0.494845 0.816667
58 NAG MAN BMA MAN NAG GAL 0.49 0.90566
59 NAG GAL GAL NAG 0.488636 0.90566
60 GAL NAG GAL NAG GAL NAG 0.488636 0.924528
61 NAG GAL BGC 0.488372 0.849057
62 NAG MAN 0.4875 0.886792
63 GLC GAL NAG GAL 0.483146 0.849057
64 LAT NAG GAL 0.483146 0.849057
65 NGT NAG 0.482759 0.761905
66 NAG BMA NAG MAN MAN NAG NAG 0.480392 0.924528
67 NGA GLA GAL BGC 0.477778 0.849057
68 AH0 NAG 0.477273 0.844828
69 SN5 SN5 0.475 0.754386
70 GUM 0.474227 0.816667
71 NAG MAN MAN 0.465909 0.849057
72 NAG MAN MMA 0.465116 0.851852
73 2F8 0.464789 0.796296
74 MAG 0.464789 0.796296
75 NAG MAN MAN MAN NAG 0.462366 0.90566
76 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.461538 0.924528
77 NAG MUB 0.460674 0.907407
78 NAG AMU 0.460674 0.907407
79 FUC GAL A2G 0.45977 0.867925
80 A2G GLA FUC 0.45977 0.867925
81 A2G GAL FUC 0.45977 0.867925
82 FUC GLA A2G 0.45977 0.867925
83 NGA GAL FUC 0.45977 0.867925
84 NG1 0.459459 0.709677
85 GN1 0.459459 0.709677
86 A2G GAL NAG FUC 0.458333 0.924528
87 FUC GAL NAG A2G 0.458333 0.924528
88 NAG NAG BMA MAN MAN NAG GAL NAG 0.457944 0.924528
89 NAG NM9 0.454545 0.890909
90 FHY 0.452632 0.859649
91 NAG AH0 0.451613 0.844828
92 NA1 NAA AMI 0.45098 0.7
93 NAG MAN BMA NDG MAN NAG GAL 0.448598 0.924528
94 JXD 0.447619 0.728571
95 GAL NDG 0.443038 0.849057
96 NDG GAL 0.443038 0.849057
97 NLC 0.443038 0.849057
98 5AX 0.442857 0.830189
99 NAG NAG BMA MAN MAN 0.44 0.90566
100 FUC BGC GAL NAG GAL 0.44 0.867925
101 NDG BDP BDP NPO NDG 0.439252 0.720588
102 MMA MAN NAG MAN NAG NAG 0.4375 0.907407
103 FUC BGC GAL NAG 0.4375 0.867925
104 BMA Z4Y NAG 0.43617 0.833333
105 BGC FUC GAL FUC A2G 0.43299 0.886792
106 GLC FUC GAL FUC A2G 0.43299 0.886792
107 GYU 0.432099 0.813559
108 A2G GAL BGC FUC 0.428571 0.867925
109 FUC NAG GAL 0.426966 0.943396
110 SIA GAL NAG 0.425926 0.963636
111 FUC C4W NAG BMA 0.425743 0.875
112 8VZ 0.425 0.888889
113 FUC C4W NAG BMA MAN NAG 0.424779 0.875
114 SN5 SN5 NGT 0.421053 0.6875
115 3YW 0.4125 0.811321
116 FUC NAG 0.411765 0.924528
117 ASN NAG NAG BMA MAN MAN NAG NAG 0.40678 0.894737
118 LEC NGA 0.40625 0.720588
119 NAG GAL FUC FUC A2G 0.405941 0.924528
120 FUC GAL NAG A2G FUC 0.405941 0.924528
121 NAG BDP NAG BDP NAG BDP NAG 0.40404 0.907407
122 NAG MAN MAN MAN NAG GAL NAG GAL 0.401869 0.924528
123 MAN BMA NAG NAG MAN NAG GAL GAL 0.401869 0.924528
124 MA8 0.4 0.821429
125 ALA NAG AH0 DAL 0.4 0.830508
126 FUC C4W NAG BMA MAN MAN NAG NAG 0.4 0.875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DYG; Ligand: MES; Similar sites found with APoc: 128
This union binding pocket(no: 1) in the query (biounit: 4dyg.bio2) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 6FHQ DE5 None
2 1JQY A32 None
3 4XFM THE 1.22951
4 4QAC KK3 1.38249
5 4IAE 1DX 1.5873
6 4CFP NAG AMU NAG AMV 1.63934
7 5ZI2 NAD 2.04918
8 4XF6 ADP 2.04918
9 4YKI GLY 2.04918
10 1RHC F42 ACN 2.04918
11 5ZI2 ADP 2.04918
12 5WDR GNP 2.33918
13 4HJY NAG NAG NAG 2.42718
14 2JAH NDP 2.45902
15 1I36 NAP 2.45902
16 4J7U YTZ 2.45902
17 4J7U NAP 2.45902
18 6H1U ASP 2.45902
19 6BII NAP 2.45902
20 5KTI TRE 6X6 2.68456
21 1YZN GNP 2.7027
22 4PJ3 ANP 2.86885
23 2OI2 DP6 2.86885
24 1D0L BLG 2.86885
25 5XLS URA 2.86885
26 1FC4 AKB PLP 2.86885
27 4M7T SAM 2.86885
28 4POW OP1 2.86885
29 4CQM NAP 2.86885
30 1ORR NAD 2.86885
31 2IO8 ADP 2.86885
32 5OVK NDP 2.86885
33 1VLJ NAP 2.86885
34 1XS1 DUT 3.10881
35 1CT9 GLN 3.27869
36 4CTA ATP 3.27869
37 3B99 U51 3.27869
38 2H5Z CTO 3.27869
39 3FXU TSU 3.27869
40 2AE2 NAP 3.27869
41 2AE2 PTO 3.27869
42 6CQF F97 3.367
43 6G96 ACO 3.40909
44 2B3D FAD 3.43137
45 4ZV1 ARG 3.43348
46 2QTZ FAD 3.68852
47 2QTZ NAP 3.68852
48 1ZQ9 SAM 3.68852
49 4YRY FAD 3.68852
50 4FN4 NAD 3.68852
51 4I53 1C1 3.68852
52 2EWM NAD 3.68852
53 1AE1 NAP 3.68852
54 1IY8 NAD 3.68852
55 3CT5 NAG NAG NAG 3.77358
56 3SJ7 NDP 3.96825
57 3N7O N7O 3.9823
58 4WQ2 3SU 4.04624
59 1Q5H DUD 4.08163
60 5M3E APR 4.09836
61 4DJA FAD 4.09836
62 4DJA DLZ 4.09836
63 3C6K SPD 4.09836
64 3C6K MTA 4.09836
65 6GE9 ACO 4.09836
66 3A28 NAD 4.26357
67 5D2H AKG 4.5082
68 4XGX ADP 4.5082
69 3LOO B4P 4.5082
70 4X60 SFG 4.5082
71 4X60 3XV 4.5082
72 1BB6 UMG 4.65116
73 1LSZ NDG NAG NAG NAG 4.7619
74 3O9L LPN 4.81928
75 1UZN NAP 4.91803
76 2GDZ NAD 4.91803
77 4ZA2 NAD 4.91803
78 1XC6 GAL 4.91803
79 1J5P NAD 4.91803
80 4QED NAP 4.91803
81 4ZM4 PLP 4.91803
82 2PYY GLU 5.26316
83 5TO8 7FM 5.32787
84 3OGV PTQ 5.32787
85 3WQT ANP 5.32787
86 5O2N NAG NAG NDG NAG 5.32787
87 5O2N NAG 5.32787
88 4ITU NAI 5.32787
89 3VZS NAP 5.32787
90 3GDN FAD 5.32787
91 3GDN HBX 5.32787
92 1GEG NAD 5.32787
93 5L9O GOP 5.59701
94 4NBU NAI 5.6
95 3EJR HN4 5.7377
96 1Z08 GNP 5.88235
97 1RX0 FAD 6.14754
98 2DTX BMA 6.14754
99 5ULJ 0WD 6.14754
100 1LZR NAG NAG NAG NAG 6.15385
101 1Q23 FUA 6.39269
102 154L NAG NAG NAG 6.48649
103 6CFC BLG 6.55738
104 5DEY 59T 6.55738
105 3IPQ 965 6.96721
106 6BJ3 ILE PRO LEU THR GLU GLU ALA GLU LEU 7.07071
107 2YAK OSV 7.78689
108 1U7T NAD 7.78689
109 2JAP NDP 8.09717
110 2QX0 APC 8.1761
111 5KKA 6V0 8.19672
112 2GK6 ADP 8.19672
113 4K81 GTP 8.19672
114 1T7Q 152 8.60656
115 1T7Q COA 8.60656
116 4DVR 0LY 9.43396
117 4GV8 DUP 9.46746
118 2GYI HYA 9.83607
119 3F8K COA 10
120 5UKL SIX 11.0656
121 5XCS TYR PRO TYR ASP VAL PRO ASP TYR ALA 12.2093
122 2JDC CAO 13.0137
123 4OI4 ATP 13.1148
124 4WX0 HXD 14.3443
125 3O03 NAP 15.5738
126 3AFH GSU 15.5738
127 4RI1 ACO 17.2043
128 4OOP DUP 19.2771
Pocket No.: 2; Query (leader) PDB : 4DYG; Ligand: NAG NAG NAG NAG; Similar sites found with APoc: 26
This union binding pocket(no: 2) in the query (biounit: 4dyg.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2PT9 2MH 1.22951
2 5CUQ NSC 2.04918
3 4OUJ LBT 2.45902
4 5DOZ NDP 2.45902
5 4U7W NDP 2.45902
6 5Z2L NDP 2.45902
7 3AFN NAP 2.86885
8 1LDN NAD 3.27869
9 5WHU SIA GAL 3.3557
10 6FA4 GNP 3.46821
11 4OSP NAP 3.68852
12 4JD3 COA 4.09836
13 4JD3 PLM 4.09836
14 1SOW NAD 4.09836
15 1PR9 NAP 4.09836
16 5EPO NAP 4.09836
17 1XKQ NDP 4.91803
18 2CFC NAD 5.32787
19 3T34 GDP 5.32787
20 1V7C HEY 5.7377
21 5EOB 5QQ 6.14754
22 5I34 GDP 6.55738
23 6G28 AR6 9.01639
24 1PZG A3D 9.42623
25 2Z3Y F2N 11.8852
26 3O03 NAP 15.5738
Pocket No.: 3; Query (leader) PDB : 4DYG; Ligand: MES; Similar sites found with APoc: 19
This union binding pocket(no: 3) in the query (biounit: 4dyg.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 5N1X 8HH None
2 1FDJ 13P 0.819672
3 1RZM E4P 2.04918
4 1R6N 434 2.36967
5 4OUJ LBT 2.45902
6 4CME KTZ 2.86885
7 1JJV ATP 2.91262
8 4RJD TFP 3.0303
9 3WCS MAN NAG 3.68852
10 3VPD BUA 4.09836
11 5ABX MGP 4.21053
12 1KYV RBF 4.40252
13 3O01 DXC 4.5082
14 3HYW DCQ 4.91803
15 1NU4 MLA 5.15464
16 3KPE TM3 7.69231
17 1RVV INI 7.79221
18 1DNA CB3 10.6557
19 4UEC MGT 11.413
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