Receptor
PDB id Resolution Class Description Source Keywords
1UR8 1.9 Å EC: 3.2.1.14 INTERACTIONS OF A FAMILY 18 CHITINASE WITH THE DESIGNED INHI HM508, AND ITS DEGRADATION PRODUCT, CHITOBIONO-DELTA-LACTON SERRATIA MARCESCENS HYDROLASE CHITINASE INHIBITION LACTONE CHITIN DEGRADATIOGLYCOSIDASE
Ref.: INTERACTIONS OF A FAMILY 18 CHITINASE WITH THE DESI INHIBITOR HM508 AND ITS DEGRADATION PRODUCT, CHITOBIONO-DELTA-LACTONE. J.BIOL.CHEM. V. 279 3612 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1499;
A:1500;
A:1501;
B:1500;
B:1501;
B:1502;
B:1503;
B:1504;
B:1505;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:1503;
A:1504;
A:1505;
B:1507;
B:1508;
B:1509;
B:1510;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
GDL NAG C:1;
D:1;
Valid;
Valid;
none;
none;
Ki = 45 uM
424.403 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WD1 2.3 Å EC: 3.2.1.14 SERRATIA MARCESCENS CHITINASE B COMPLEXED WITH SYN-TRIAZOLE SERRATIA MARCESCENS TIM BARREL HYDROLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: OBSERVATION OF THE CONTROLLED ASSEMBLY OF PRECLICK COMPONENTS IN THE IN SITU CLICK CHEMISTRY GENERATIO CHITINASE INHIBITOR PROC.NATL.ACAD.SCI.USA V. 110 15892 2013
Members (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3WD4 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
2 6JKF Kd = 0.19 uM BV0 C24 H25 N6 O3 CC1=CC=CN2....
3 1UR9 Ki = 1.7 uM GDL PHJ NAG n/a n/a
4 1W1Y ic50 = 2.4 mM TYP C14 H16 N2 O3 c1cc(ccc1C....
5 6JK9 Ki = 0.41 uM BU0 C27 H25 N5 O2 C[C@@H](c1....
6 1H0G - 0AR DPR HSE HIS UN1 n/a n/a
7 1E6N - NAG NAG NAG NAG NAG n/a n/a
8 4Z2H ic50 = 8.3 uM M6A C33 H57 N5 O10 [H]/N=C(NC....
9 4Z2K - M6E C38 H67 N5 O10 [H]/N=C(/N....
10 3WD2 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
11 1E6Z - NAG NAG n/a n/a
12 7C34 Ki = 11.79 uM BER C20 H18 N O4 COc1ccc2cc....
13 1W1V ic50 = 6.3 mM ALJ C11 H19 N5 O2 C1C[C@H]2C....
14 3WD1 ic50 = 0.022 uM ST7 C37 H41 N11 O4 [H]/N=C(/N....
15 3WD3 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
16 1H0I - VR0 MEA IAS IAS DAL n/a n/a
17 1E6R - NAA AMI NAA n/a n/a
18 4Z2I ic50 = 0.036 uM M6B C34 H59 N5 O10 [H]/N=C(NC....
19 1O6I Ki = 0.65 mM 0HZ C11 H20 N5 O2 NULL
20 1W1P ic50 = 5 mM GIO C7 H10 N2 O2 C1C[C@H]2C....
21 1W1T ic50 = 1.1 mM CHQ C11 H14 N4 O2 c1c([nH]cn....
22 1UR8 Ki = 45 uM GDL NAG n/a n/a
23 4Z2L - M6F C31 H55 N5 O10 [H]/N=C(NC....
24 1OGG Ki = 6.4 uM NAA AMI NAA n/a n/a
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 3WD4 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
2 6JKF Kd = 0.19 uM BV0 C24 H25 N6 O3 CC1=CC=CN2....
3 1UR9 Ki = 1.7 uM GDL PHJ NAG n/a n/a
4 1W1Y ic50 = 2.4 mM TYP C14 H16 N2 O3 c1cc(ccc1C....
5 6JK9 Ki = 0.41 uM BU0 C27 H25 N5 O2 C[C@@H](c1....
6 1H0G - 0AR DPR HSE HIS UN1 n/a n/a
7 1E6N - NAG NAG NAG NAG NAG n/a n/a
8 4Z2H ic50 = 8.3 uM M6A C33 H57 N5 O10 [H]/N=C(NC....
9 4Z2K - M6E C38 H67 N5 O10 [H]/N=C(/N....
10 3WD2 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
11 1E6Z - NAG NAG n/a n/a
12 7C34 Ki = 11.79 uM BER C20 H18 N O4 COc1ccc2cc....
13 1W1V ic50 = 6.3 mM ALJ C11 H19 N5 O2 C1C[C@H]2C....
14 3WD1 ic50 = 0.022 uM ST7 C37 H41 N11 O4 [H]/N=C(/N....
15 3WD3 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
16 1H0I - VR0 MEA IAS IAS DAL n/a n/a
17 1E6R - NAA AMI NAA n/a n/a
18 4Z2I ic50 = 0.036 uM M6B C34 H59 N5 O10 [H]/N=C(NC....
19 1O6I Ki = 0.65 mM 0HZ C11 H20 N5 O2 NULL
20 1W1P ic50 = 5 mM GIO C7 H10 N2 O2 C1C[C@H]2C....
21 1W1T ic50 = 1.1 mM CHQ C11 H14 N4 O2 c1c([nH]cn....
22 1UR8 Ki = 45 uM GDL NAG n/a n/a
23 4Z2L - M6F C31 H55 N5 O10 [H]/N=C(NC....
24 1OGG Ki = 6.4 uM NAA AMI NAA n/a n/a
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 3WD4 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
2 6JKF Kd = 0.19 uM BV0 C24 H25 N6 O3 CC1=CC=CN2....
3 1UR9 Ki = 1.7 uM GDL PHJ NAG n/a n/a
4 1W1Y ic50 = 2.4 mM TYP C14 H16 N2 O3 c1cc(ccc1C....
5 6JK9 Ki = 0.41 uM BU0 C27 H25 N5 O2 C[C@@H](c1....
6 1H0G - 0AR DPR HSE HIS UN1 n/a n/a
7 1E6N - NAG NAG NAG NAG NAG n/a n/a
8 4Z2H ic50 = 8.3 uM M6A C33 H57 N5 O10 [H]/N=C(NC....
9 4Z2K - M6E C38 H67 N5 O10 [H]/N=C(/N....
10 3WD2 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
11 1E6Z - NAG NAG n/a n/a
12 7C34 Ki = 11.79 uM BER C20 H18 N O4 COc1ccc2cc....
13 1W1V ic50 = 6.3 mM ALJ C11 H19 N5 O2 C1C[C@H]2C....
14 3WD1 ic50 = 0.022 uM ST7 C37 H41 N11 O4 [H]/N=C(/N....
15 3WD3 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
16 1H0I - VR0 MEA IAS IAS DAL n/a n/a
17 1E6R - NAA AMI NAA n/a n/a
18 4Z2I ic50 = 0.036 uM M6B C34 H59 N5 O10 [H]/N=C(NC....
19 1O6I Ki = 0.65 mM 0HZ C11 H20 N5 O2 NULL
20 1W1P ic50 = 5 mM GIO C7 H10 N2 O2 C1C[C@H]2C....
21 1W1T ic50 = 1.1 mM CHQ C11 H14 N4 O2 c1c([nH]cn....
22 1UR8 Ki = 45 uM GDL NAG n/a n/a
23 4Z2L - M6F C31 H55 N5 O10 [H]/N=C(NC....
24 1OGG Ki = 6.4 uM NAA AMI NAA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GDL NAG; Similar ligands found: 157
No: Ligand ECFP6 Tc MDL keys Tc
1 GDL NAG 1 1
2 NDG NAG NAG NAG NAG 0.929825 0.979592
3 NAG NAG NAG NAG NAG NAG 0.929825 0.979592
4 NAG NAG NAG NAG NAG NAG NAG NAG 0.929825 0.979592
5 NAG NAG NAG NAG NAG 0.929825 0.979592
6 NAG GAL NAG 0.8 1
7 SN5 SN5 0.725806 0.826923
8 NAG GAL 0.716667 0.9375
9 NAG NAG BMA MAN NAG 0.688312 0.979592
10 NDG NAG 0.6875 0.979592
11 NAG NAG NAG TMX 0.685714 0.827586
12 BGC GAL NGA 0.661765 0.9375
13 A2G NAG 0.65625 1
14 MAN NAG 0.650794 0.9375
15 MBG A2G 0.646154 0.938776
16 NAG GAL NAG GAL 0.643836 1
17 NAG GAL NAG GAL NAG GAL 0.643836 0.979592
18 NAG NAG NAG NAG NAG NAG NAG 0.625 0.90566
19 NAG NAG NAG 0.625 0.90566
20 NAG NAG NAG NAG 0.625 0.90566
21 NAG GAL GAL 0.623188 0.9375
22 BMA MAN NAG 0.611111 0.9375
23 NAG NAG 0.608696 0.979592
24 BGC GAL NAG 0.60274 0.9375
25 NAG GAL FUC A2G 0.597222 0.958333
26 GAL NGA 0.588235 0.88
27 AMU NAG 0.586667 0.96
28 Z3Q NGA 0.586667 0.813559
29 MBG NAG 0.58209 0.938776
30 GAL NGA A2G 0.577465 1
31 NAG NAG BMA MAN MAN NAG GAL NAG 0.576087 0.979592
32 NAG G6S 0.575342 0.71875
33 NAG NOJ NAG 0.571429 0.872727
34 Z4S NAG NAG 0.571429 0.90566
35 NAG NOJ NAG NAG 0.571429 0.857143
36 NAG NGO 0.567568 0.87037
37 NDG BMA MAN MAN NAG GAL NAG 0.565217 0.979592
38 NAG NAG MAN MAN MAN 0.564706 1
39 BGC GAL GLA NGA 0.564103 0.9375
40 NDG BMA MAN MAN NAG MAN MAN 0.55914 1
41 NGT NAG 0.552632 0.79661
42 2F8 0.55 0.877551
43 6Y2 0.55 0.75
44 NAG NGT NAG 0.55 0.813559
45 MAG 0.55 0.877551
46 3QL 0.547945 0.923077
47 GAL FUC A2G 0.546667 0.958333
48 HSQ 0.54386 0.833333
49 NDG 0.54386 0.833333
50 A2G 0.54386 0.833333
51 NGA 0.54386 0.833333
52 NAG 0.54386 0.833333
53 BM3 0.54386 0.833333
54 MAN NAG GAL 0.540541 0.9375
55 MAN MAN NAG 0.539474 0.9
56 GAL NAG GAL 0.533333 0.9375
57 MMA MAN NAG 0.533333 0.938776
58 NAG GAL FUC GLA 0.530864 0.958333
59 KPM 0.53012 0.903846
60 AMV NAG AMU NAG 0.53012 0.941176
61 NAG GAL UNU 0.525 0.94
62 MAN MAN MAN NAG NAG 0.52439 1
63 NM9 NAG 0.519481 0.941176
64 BGC GAL FUC A2G 0.517647 0.958333
65 NG1 0.515625 0.741379
66 GN1 0.515625 0.741379
67 NAG GAL BGC GAL 0.512821 0.9375
68 BMA Z4Y NAG 0.512195 0.918367
69 AO3 0.511628 0.738462
70 NAA AMI NAA 0.511628 0.738462
71 NAG BMA MAN MAN NAG GAL NAG GAL 0.51087 0.979592
72 ASG 0.507692 0.65625
73 AH0 NAG 0.506329 0.888889
74 NAG NAG BMA 0.506329 0.923077
75 NAG GCS GCS 0.506173 0.901961
76 NAG FUC GAL FUC A2G 0.505747 0.979592
77 NAG GAL FUC FUC A2G 0.505747 0.979592
78 GUM 0.5 0.857143
79 GAL NAG GAL NAG GAL 0.5 1
80 NAG BMA MAN MAN MAN MAN 0.494253 0.9375
81 BGC FUC GAL NAG 0.494118 0.958333
82 TVD GAL 0.492754 0.979592
83 UMG 0.488889 0.857143
84 BGC FUC GAL FUC A2G 0.488372 0.938776
85 NAG BDP NAG BDP NAG BDP NAG 0.488372 0.96
86 NAG GAL GLC NAG GLC RAM 0.488095 1
87 GAL NAG 0.486111 0.9375
88 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.484848 1
89 BMA MAN MAN NAG GAL NAG 0.483871 1
90 BGC GAL NGA GAL 0.481013 0.9375
91 BMX BMX BMX BM3 0.481013 0.842105
92 GYU 0.478873 0.821429
93 3YW 0.478261 0.857143
94 MMA MAN NAG MAN NAG NAG 0.476744 0.96
95 NAG GAL BEK 0.47191 0.842105
96 A2G GAL 0.471429 0.9375
97 A2G GAL NAG 0.469136 1
98 NAG GCU NAG GCD 0.463918 0.888889
99 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.462366 0.9375
100 MA8 0.459459 0.830189
101 MUB ALA NAG DGN 0.459184 0.872727
102 LEC NGA 0.458824 0.75
103 NAG AH0 0.458824 0.888889
104 SER A2G 0.458333 0.865385
105 TNR 0.458333 0.882353
106 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.457447 0.9375
107 NAG NAG BMA MAN 0.454545 0.923077
108 AMU ALA NAG DGL 0.453608 0.888889
109 JXD 0.453608 0.705882
110 BGC GAL NAG GAL 0.451219 0.9375
111 GLC GAL NAG GAL FUC A2G 0.44898 0.979592
112 MUB ALA NAG ZGL 0.44898 0.872727
113 BGC GAL NAG NAG GAL GAL 0.445652 1
114 MUB ALA NAG GLN 0.444444 0.888889
115 FHY 0.443182 0.90566
116 NAG FUC GAL 0.443038 0.958333
117 NAG NAG BMA BMA 0.44186 0.888889
118 NAG NAG BMA MAN MAN NAG NAG 0.441176 0.90566
119 NDG FUC GAL FUC 0.439024 0.938776
120 NAG GAL FUC FUC 0.439024 0.938776
121 GYP GZL NAG 0.438202 0.884615
122 HSH A2G FUC 0.438202 0.807018
123 YZ0 MAN MAN NAG MAN 0.434783 0.938776
124 GDL PHJ NAG 0.431579 0.786885
125 SNG 0.430769 0.803922
126 GYT 0.43038 0.813559
127 BGC GAL GLA NGA GAL 0.430233 0.9375
128 BGC FUC GAL NAG GAL 0.430108 0.958333
129 BDP NPO NDG BDP NDG 0.43 0.75
130 NDG NAG GLA NAG GLC RAM 0.43 0.979592
131 NDG GLA NAG GLC RAM 0.43 0.979592
132 NAA AMI NA1 0.427083 0.727273
133 SN5 NGT SN5 0.425287 0.716667
134 GAL SIA NGA 0.424242 0.923077
135 LEC 0.423077 0.703125
136 6ZC 0.423077 0.703125
137 SN5 NGT 0.421687 0.716667
138 NDG GLA GLC NAG GLC RAM 0.417476 0.979592
139 C4W NAG FUC BMA MAN NAG 0.415094 0.923077
140 C4W NAG FUC BMA 0.414894 0.923077
141 NAG GAL FUC 0.414634 0.958333
142 NAG GAL SIA 0.414141 0.923077
143 NAG GAL NGC 0.413462 0.886792
144 NAG BMA 0.413333 0.846154
145 16G 0.411765 0.724138
146 4QY 0.411765 0.724138
147 YX1 0.411765 0.646154
148 BMX 0.411765 0.724138
149 MGC GAL 0.410959 0.938776
150 HD4 0.407407 0.733333
151 NAG GAL NAG GAL SIA 0.40708 0.90566
152 STZ 0.405797 0.671875
153 BGC GAL NAG GAL FUC 0.404255 0.958333
154 BGC GAL SIA NAG 0.40367 0.923077
155 57S 0.402439 0.733333
156 ALA NAG AH0 DAL 0.402062 0.872727
157 NAG FUC 0.4 0.9375
Similar Ligands (3D)
Ligand no: 1; Ligand: GDL NAG; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WD1; Ligand: ST7; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 3wd1.bio1) has 72 residues
No: Leader PDB Ligand Sequence Similarity
1 5Y2C NAG NAG NAG NAG NAG 39.6867
2 1NWU NAG NAG NAG NDG 47.7901
Pocket No.: 2; Query (leader) PDB : 3WD1; Ligand: ST7; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 3wd1.bio2) has 72 residues
No: Leader PDB Ligand Sequence Similarity
1 6JMN BV0 32.7968
2 5Y2C NAG NAG NAG NAG NAG 39.6867
3 6HM1 AO3 42.75
4 1NWU NAG NAG NAG NDG 47.7901
5 6KXL NAG 48.9247
Pocket No.: 3; Query (leader) PDB : 3WD1; Ligand: ST7; 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: 3wd1.bio2) has 72 residues
No: Leader PDB Ligand Sequence Similarity
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