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Receptor
PDB id Resolution Class Description Source Keywords
4P8X 2.48 Å EC: 3.-.-.- THE CRYSTAL STRUCTURES OF YKL-39 IN THE PRESENCE OF CHITOOLIGOSACCHARIDES (GLCNAC6) WERE SOLVED TO RESOLUTIONS A NGSTROM HOMO SAPIENS CHITINASE 3-LIKE PROTEIN 2 HUMAN YKL-39 FAMILY-18 CHITINAS
Ref.: STRUCTURAL AND THERMODYNAMIC INSIGHTS INTO CHITOOLIGOSACCHARIDE BINDING TO HUMAN CARTILAGE CHI 3-LIKE PROTEIN 2 (CHI3L2 OR YKL-39). J.BIOL.CHEM. V. 290 2617 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:409;
A:408;
A:407;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
NAG NAG NAG NAG NAG NAG A:401;
Valid;
none;
Kd = 0.04 uM
1237.18 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4P8X 2.48 Å EC: 3.-.-.- THE CRYSTAL STRUCTURES OF YKL-39 IN THE PRESENCE OF CHITOOLIGOSACCHARIDES (GLCNAC6) WERE SOLVED TO RESOLUTIONS A NGSTROM HOMO SAPIENS CHITINASE 3-LIKE PROTEIN 2 HUMAN YKL-39 FAMILY-18 CHITINAS
Ref.: STRUCTURAL AND THERMODYNAMIC INSIGHTS INTO CHITOOLIGOSACCHARIDE BINDING TO HUMAN CARTILAGE CHI 3-LIKE PROTEIN 2 (CHI3L2 OR YKL-39). J.BIOL.CHEM. V. 290 2617 2015
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 4P8V Kd = 204 uM NAG NAG n/a n/a
2 4AY1 - NAG NAG NAG NAG n/a n/a
3 4P8X Kd = 0.04 uM NAG NAG NAG NAG NAG NAG n/a n/a
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 1NWT - NAG NAG NAG NAG NDG NAG n/a n/a
2 1NWU - NAG NAG NAG NDG n/a n/a
3 1HJW - NAG NAG NAG NAG NAG n/a n/a
4 1ZBC - TRP PRO TRP n/a n/a
5 2DT0 - NAG NAG NAG n/a n/a
6 2DT1 - NAG NAG NAG NAG n/a n/a
7 2DT3 Kd = 18 uM NAG NAG NAG NAG NAG NAG n/a n/a
8 1WAW ic50 = 0.013 uM 0AR DPR ASP HIS UN1 n/a n/a
9 1WB0 ic50 = 4.5 uM VR0 MEA IAS IAS DAL n/a n/a
10 4WKH - CBS C16 H28 N2 O11 CC(=O)N[C@....
11 1HKK ic50 = 40 nM NAA NAA AMI n/a n/a
12 4WK9 - CBS C16 H28 N2 O11 CC(=O)N[C@....
13 5NRF ic50 = 163 nM 95Q C22 H27 Cl N6 c1ccc(cc1)....
14 4WKF - CBS C16 H28 N2 O11 CC(=O)N[C@....
15 5NR8 ic50 = 175 nM 95N C16 H23 Br N6 CN(CCc1ccc....
16 5NRA ic50 = 123 nM 95K C19 H29 Br N6 CC(C)CN(CC....
17 2YBT ic50 = 20 uM DW0 C17 H20 N8 O4 Cn1cnc2c1C....
18 3RM4 ic50 = 0.21 uM 3RM C14 H19 Br N6 O c1cc(ccc1O....
19 3RM9 ic50 = 13 uM 613 C11 H15 Cl N4 [H]/N=C(N)....
20 2YBU Ki = 0.42 uM CX9 C16 H18 N8 O4 Cn1cnc2c1C....
21 3RME ic50 = 22 uM RME C13 H20 N4 O CCNC(=O)c1....
22 3FY1 - NA1 NAA AMI n/a n/a
23 4P8V Kd = 204 uM NAG NAG n/a n/a
24 4AY1 - NAG NAG NAG NAG n/a n/a
25 4P8X Kd = 0.04 uM NAG NAG NAG NAG NAG NAG n/a n/a
50% Homology Family (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 5Y2B - NAG NAG NAG NAG NAG NAG NAG n/a n/a
2 1NWT - NAG NAG NAG NAG NDG NAG n/a n/a
3 1NWU - NAG NAG NAG NDG n/a n/a
4 1HJW - NAG NAG NAG NAG NAG n/a n/a
5 3WQV Kd = 6.2 uM GCS GCS GCS GCS GCS n/a n/a
6 3WQW - GCS GCS GCS GCS GCS n/a n/a
7 1ZB5 - TRP PRO TRP n/a n/a
8 2DSU - NDG NAG NAG n/a n/a
9 1ZBC - TRP PRO TRP n/a n/a
10 2DT0 - NAG NAG NAG n/a n/a
11 2DT1 - NAG NAG NAG NAG n/a n/a
12 2DT3 Kd = 18 uM NAG NAG NAG NAG NAG NAG n/a n/a
13 1WAW ic50 = 0.013 uM 0AR DPR ASP HIS UN1 n/a n/a
14 1WB0 ic50 = 4.5 uM VR0 MEA IAS IAS DAL n/a n/a
15 5Y2C - NAG NAG NAG NAG NAG n/a n/a
16 4WKH - CBS C16 H28 N2 O11 CC(=O)N[C@....
17 1HKK ic50 = 40 nM NAA NAA AMI n/a n/a
18 4WK9 - CBS C16 H28 N2 O11 CC(=O)N[C@....
19 5NRF ic50 = 163 nM 95Q C22 H27 Cl N6 c1ccc(cc1)....
20 4WKF - CBS C16 H28 N2 O11 CC(=O)N[C@....
21 5NR8 ic50 = 175 nM 95N C16 H23 Br N6 CN(CCc1ccc....
22 5NRA ic50 = 123 nM 95K C19 H29 Br N6 CC(C)CN(CC....
23 3RM8 ic50 = 0.7 uM RM8 C19 H22 N4 Cc1c(c2ccc....
24 2YBT ic50 = 20 uM DW0 C17 H20 N8 O4 Cn1cnc2c1C....
25 3RM4 ic50 = 0.21 uM 3RM C14 H19 Br N6 O c1cc(ccc1O....
26 3RM9 ic50 = 13 uM 613 C11 H15 Cl N4 [H]/N=C(N)....
27 2YBU Ki = 0.42 uM CX9 C16 H18 N8 O4 Cn1cnc2c1C....
28 3RME ic50 = 22 uM RME C13 H20 N4 O CCNC(=O)c1....
29 3FY1 - NA1 NAA AMI n/a n/a
30 4P8V Kd = 204 uM NAG NAG n/a n/a
31 4AY1 - NAG NAG NAG NAG n/a n/a
32 4P8X Kd = 0.04 uM NAG NAG NAG NAG NAG NAG n/a n/a
33 4R5E Kd = 0.00000145 M AO3 C25 H42 N4 O14 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAG NAG NAG NAG NAG NAG; Similar ligands found: 188
No: Ligand ECFP6 Tc MDL keys Tc
1 NDG NAG NAG 1 1
2 CTO 1 1
3 NAG NAG NAG NAG NAG NAG 1 1
4 NAG NAG NDG 1 1
5 NAG NAG NAG NAG NAG NAG NAG NAG 1 1
6 NDG NAG NAG NAG 1 1
7 NAG NAG NAG NAG NDG 1 1
8 NAG NAG NAG NDG 1 1
9 NDG NAG NAG NDG 1 1
10 NAG NAG NDG NAG 1 1
11 NAG NAG NAG NAG NAG 1 1
12 NAG GDL 0.929825 0.979592
13 NDG NAG 0.929825 0.979592
14 CBS 0.929825 0.979592
15 CBS CBS 0.929825 0.979592
16 NAG GAL NAG 0.753623 0.979592
17 TCG 0.742857 0.844828
18 NAG GAL GAL NAG 0.69863 0.979592
19 GAL NAG GAL NAG GAL NAG 0.69863 1
20 SN5 SN5 0.681818 0.811321
21 NAG NAG NAG NAG 0.680556 0.924528
22 NAG NAG NAG 0.680556 0.924528
23 NLC 0.671875 0.918367
24 NDG GAL 0.671875 0.918367
25 GAL NDG 0.671875 0.918367
26 NAG BMA NAG MAN MAN NAG NAG 0.655172 1
27 NGA GAL BGC 0.647887 0.918367
28 FUC GAL NAG A2G 0.641975 1
29 A2G GAL NAG FUC 0.641975 1
30 MBG A2G 0.632353 0.92
31 A2G MBG 0.632353 0.92
32 NOJ NAG NAG NAG 0.623377 0.875
33 Z4S NAG NAG 0.623377 0.924528
34 NOJ NAG NAG 0.623377 0.857143
35 NAG NAG BMA MAN MAN NAG GAL NAG 0.619565 1
36 NAG A2G 0.617647 0.979592
37 NAG NGA 0.617647 0.979592
38 NAG NAG BMA MAN MAN 0.611765 0.979592
39 NAG MAN BMA NDG MAN NAG GAL 0.608696 1
40 NAG GAL 0.602941 0.918367
41 GAL NAG 0.602941 0.918367
42 NAG NAG NGT 0.6 0.830508
43 GAL NAG MAN 0.594595 0.918367
44 DLD 0.589744 0.813559
45 MAN BMA NAG 0.589041 0.918367
46 GLA GAL NAG 0.589041 0.918367
47 NAG NDG 0.583333 0.886792
48 NAG NAG 0.583333 0.886792
49 NAG FUC 0.57971 0.897959
50 NAG AMU NAG AMV 0.578313 0.960784
51 NAG GAL BGC 0.571429 0.918367
52 DR2 0.565789 0.938776
53 FUC GAL NDG 0.565789 0.938776
54 NDG GAL FUC 0.565789 0.938776
55 FUC GAL NAG 0.565789 0.938776
56 FUL GAL NAG 0.565789 0.938776
57 NAG GAL FUC 0.565789 0.938776
58 GAL NAG FUC 0.565789 0.938776
59 LAT NAG GAL 0.5625 0.918367
60 GLC GAL NAG GAL 0.5625 0.918367
61 6Y2 0.560976 0.765625
62 NAA NAA AMI 0.55814 0.753846
63 AO3 0.55814 0.753846
64 NAG MUB 0.556962 0.98
65 NAG AMU 0.556962 0.98
66 NAG NDG BMA 0.556962 0.90566
67 NAG NAG BMA 0.556962 0.90566
68 NGA GAL 0.555556 0.862745
69 NGA GLA GAL BGC 0.555556 0.918367
70 NAG MAN MAN MAN NAG GAL NAG GAL 0.554348 1
71 MAN BMA NAG NAG MAN NAG GAL GAL 0.554348 1
72 NAG MAN BMA 0.552632 0.918367
73 NAG GAL GAL NAG GAL 0.55 0.979592
74 NAG MBG 0.549296 0.92
75 GAL NGA A2G 0.546667 0.979592
76 G6S NAG 0.545455 0.707692
77 GAL NAG GAL 0.544304 0.882353
78 M5G 0.536082 0.979592
79 UMG 0.533333 0.875
80 NAG MAN BMA MAN NAG GAL 0.526882 0.979592
81 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.525253 0.979592
82 NAG MAN MAN 0.525 0.918367
83 NGT NAG 0.525 0.813559
84 3QL 0.519481 0.90566
85 NGA GAL FUC 0.518987 0.938776
86 FUC GAL A2G 0.518987 0.938776
87 A2G GLA FUC 0.518987 0.938776
88 FUC GLA A2G 0.518987 0.938776
89 A2G GAL FUC 0.518987 0.938776
90 NAG NAG BMA MAN NAG 0.515789 0.924528
91 2F8 0.515625 0.86
92 MAG 0.515625 0.86
93 NAG MAN 0.513514 0.959184
94 HS2 0.512821 0.882353
95 MAN MAN NAG 0.5125 0.882353
96 GUM 0.511111 0.875
97 NGA 0.508197 0.816327
98 HSQ 0.508197 0.816327
99 A2G 0.508197 0.816327
100 BM3 0.508197 0.816327
101 NDG 0.508197 0.816327
102 NAG 0.508197 0.816327
103 NAG MAN MMA 0.506329 0.92
104 GAL BGC NAG GAL 0.506173 0.918367
105 GAL NAG GAL BGC 0.505882 0.882353
106 KPM 0.505747 0.923077
107 NAG GCU NAG GCD 0.505155 0.907407
108 GCS GCS NAG 0.5 0.884615
109 NAG MAN MAN MAN NAG 0.5 0.979592
110 UNU GAL NAG 0.5 0.96
111 NAG NAG BMA MAN 0.5 0.90566
112 A2G GAL BGC FUC 0.494382 0.938776
113 NAG NM9 0.493827 0.960784
114 BMA Z4Y NAG 0.488372 0.9
115 NAG NAG BMA BMA 0.488372 0.907407
116 GN1 0.485294 0.758621
117 NG1 0.485294 0.758621
118 FUC GAL NAG A2G FUC 0.483516 1
119 NAG GAL FUC FUC A2G 0.483516 1
120 AH0 NAG 0.481928 0.907407
121 NAG NAG BMA MAN MAN NAG NAG 0.480392 0.924528
122 ASG 0.478261 0.646154
123 FUC BGC GAL NAG GAL 0.473118 0.938776
124 NAG BMA MAN MAN MAN MAN 0.472527 0.918367
125 FUC BGC GAL NAG 0.47191 0.938776
126 NDG BDP BDP NPO NDG 0.47 0.765625
127 NA1 NAA AMI 0.46875 0.742424
128 GLC FUC GAL FUC A2G 0.466667 0.959184
129 NAG BDP NAG BDP NAG BDP NAG 0.466667 0.98
130 BGC FUC GAL FUC A2G 0.466667 0.959184
131 8VZ 0.465753 0.96
132 JXD 0.464646 0.720588
133 FUC C4W NAG BMA 0.457447 0.942308
134 MMA MAN NAG MAN NAG NAG 0.455556 0.98
135 SN5 SN5 NGT 0.454545 0.733333
136 GYU 0.453333 0.807018
137 FUC C4W NAG BMA MAN NAG 0.45283 0.942308
138 3YW 0.452055 0.84
139 BEK GAL NAG 0.451613 0.859649
140 NAG AMU ALA DGL 0.45 0.907407
141 NAG A2G GAL 0.447059 0.979592
142 GAL NGA 0.445946 0.918367
143 GAL A2G 0.445946 0.918367
144 A2G GAL 0.445946 0.918367
145 NAG MU2 0.445545 0.890909
146 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.443299 0.918367
147 NAG AH0 0.438202 0.907407
148 LEC NGA 0.438202 0.765625
149 MA8 0.435897 0.814815
150 TNR 0.434211 0.865385
151 ASN NAG NAG BMA MAN MAN NAG NAG 0.432432 0.890909
152 GLC GAL NAG GAL FUC A2G 0.431373 1
153 A2G GAL NAG FUC GAL GLC 0.431373 1
154 BGC GAL NAG GAL 0.430233 0.918367
155 GAL NAG GAL GLC 0.430233 0.918367
156 GAL NGA GLA BGC GAL 0.426966 0.918367
157 BGA 0.425532 0.824561
158 FUC C4W NAG BMA MAN MAN NAG NAG 0.424779 0.942308
159 FHY 0.423913 0.924528
160 GAL NDG FUC 0.421687 0.938776
161 FUC NDG GAL 0.421687 0.938776
162 SIA GAL NGA 0.421569 0.942308
163 4U2 0.42 0.960784
164 3PV 0.419355 0.867925
165 BCW 0.418605 0.959184
166 GAL NAG FUC FUC 0.418605 0.959184
167 FUC NAG GAL FUC 0.418605 0.959184
168 FUC NDG GAL FUC 0.418605 0.959184
169 BDZ 0.418605 0.959184
170 GAL NDG FUC FUC 0.418605 0.959184
171 FUC GAL NDG FUC 0.418605 0.959184
172 FUC GAL NAG FUC 0.418605 0.959184
173 FUC C4W NAG BMA MAN 0.417476 0.942308
174 4U1 0.417476 0.942308
175 NAG GAL SIA 0.417476 0.924528
176 FUC C4W NAG BMA MAN MAN NAG 0.417391 0.942308
177 WZ5 0.416667 0.92
178 NAG GDL PHJ 0.414141 0.803279
179 NAG SIA GAL 0.411765 0.942308
180 GYT 0.409639 0.830508
181 SNG 0.405797 0.788462
182 NAG NAG BMA MAN MAN MAN MAN 0.40367 0.90566
183 6ZC 0.402439 0.71875
184 LEC 0.402439 0.71875
185 SN5 NGT 0.402299 0.733333
186 GAL BGC SIA NGA 0.401786 0.942308
187 BGC GAL SIA NGA 0.401786 0.942308
188 SIA GAL BGC NGA 0.401786 0.942308
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4P8X; Ligand: NAG NAG NAG NAG NAG NAG; Similar sites found with APoc: 23
This union binding pocket(no: 1) in the query (biounit: 4p8x.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4X9D U5P None
2 3A4X NAG NAG NAG NDG 1.92926
3 4TX6 38B 2.58065
4 4TXE 38F 3.7415
5 6C0B PAM 3.84615
6 1JXM 5GP 3.98671
7 1LLO NAA NAA AMI 4.3956
8 1TOQ AMG 4.51128
9 1JAC AMG 4.51128
10 1KUJ MMA 4.51128
11 1UGY GLA BGC 4.51128
12 1UGY GLA GLC 4.51128
13 4AKB GAL 4.51128
14 4JX1 CAH 5.66038
15 1C3V PDC 7.34694
16 2VVM PRO 9.7035
17 3N17 NAG NAG 10.2102
18 3B9A NAG NAG NAG NAG NAG NAG 38.2749
19 2WK2 SN5 SN5 NGT 39.3531
20 2WK2 SN5 SN5 39.3531
21 3G6M CFF 42.5876
22 3WD1 ST7 44.7439
23 3ALG NAG NAG NAG NAG 47.8754
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