Receptor
PDB id Resolution Class Description Source Keywords
5A2J 1.65 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH THE NAKED PEPTIDE APDTRP MUS MUSCULUS PEPTIDE BINDING PROTEIN GLYCOPEPTIDES ANTIBODIES MOLECULARECOGNITION CONFORMATION ANALYSIS FUSION PROTEIN
Ref.: DECIPHERING THE NON-EQUIVALENCE OF SERINE AND THREO GLYCOSYLATION POINTS: IMPLICATIONS FOR MOLECULAR RECOGNITION OF THE TN ANTIGEN BY AN ANTI-MUC1 ANTIB ANGEW.CHEM.INT.ED.ENGL. V. 54 9830 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO H:2111;
H:2110;
H:2108;
H:2109;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
ALA PRO ASP THR ARG PRO P:1;
Valid;
Atoms found LESS than expected: % Diff = 0.022;
submit data
640.719 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5A2J 1.65 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH THE NAKED PEPTIDE APDTRP MUS MUSCULUS PEPTIDE BINDING PROTEIN GLYCOPEPTIDES ANTIBODIES MOLECULARECOGNITION CONFORMATION ANALYSIS FUSION PROTEIN
Ref.: DECIPHERING THE NON-EQUIVALENCE OF SERINE AND THREO GLYCOSYLATION POINTS: IMPLICATIONS FOR MOLECULAR RECOGNITION OF THE TN ANTIGEN BY AN ANTI-MUC1 ANTIB ANGEW.CHEM.INT.ED.ENGL. V. 54 9830 2015
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5A2K - ALA PRO ASP THR ARG PRO A2G n/a n/a
2 5A2L - ALA PRO ASP CYS ARG PRO A2G n/a n/a
3 5A2I - ALA PRO ASP SER ARG PRO A2G n/a n/a
4 5A2J - ALA PRO ASP THR ARG PRO n/a n/a
5 5FXC - ALA PRO ASP THR ARG PRO n/a n/a
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5A2K - ALA PRO ASP THR ARG PRO A2G n/a n/a
2 5A2L - ALA PRO ASP CYS ARG PRO A2G n/a n/a
3 5A2I - ALA PRO ASP SER ARG PRO A2G n/a n/a
4 5A2J - ALA PRO ASP THR ARG PRO n/a n/a
5 5FXC - ALA PRO ASP THR ARG PRO n/a n/a
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4GQP Kd = 0.79 nM B40 C10 H15 N C[C@@H](Cc....
2 3GKZ Kd = 10 nM B40 C10 H15 N C[C@@H](Cc....
3 3GM0 Kd = 17 nM B41 C11 H15 N O2 C[C@@H](Cc....
4 4H0I - MMA C7 H14 O6 CO[C@@H]1[....
5 5J75 Ki = 0.63 nM 6GQ C19 H24 N4 O3 S Cc1ccc(cc1....
6 5A2K - ALA PRO ASP THR ARG PRO A2G n/a n/a
7 5A2L - ALA PRO ASP CYS ARG PRO A2G n/a n/a
8 5A2I - ALA PRO ASP SER ARG PRO A2G n/a n/a
9 5A2J - ALA PRO ASP THR ARG PRO n/a n/a
10 5FXC - ALA PRO ASP THR ARG PRO n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ALA PRO ASP THR ARG PRO; Similar ligands found: 92
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA PRO ASP THR ARG PRO 1 1
2 ALA PRO ASP THR ARG PRO ALA PRO 0.702703 1
3 ALA PRO ASP THR ARG PRO A2G 0.682171 0.890411
4 SER ALA PRO ASP THR ARG PRO ALA 0.666667 0.984848
5 ASP LEU THR ARG PRO 0.666667 0.925373
6 ALA PRO ASP SER ARG PRO A2G 0.638462 0.890411
7 ALA PRO ASP CYS ARG PRO A2G 0.633588 0.866667
8 ALA PRO PRO PRO ARG PRO PRO LYS PRO 0.573913 0.846154
9 GLY PRO ARG PRO 0.568627 0.830769
10 VAL VAL ARG PRO GLY SER LEU ASP LEU PRO 0.550725 0.926471
11 NGA ALA PRO ASP THR ARG PRO ALA PRO 0.526316 0.890411
12 ALA PRO ASP THR ARG PRO ALA PRO NGA 0.526316 0.890411
13 THR PRO THR ARG ASP VAL ALA THR SER PRO 0.515873 0.925373
14 GLU ARG THR ILE PRO ILE THR ARG GLU 0.503876 0.940298
15 CYS THR PRO SER ARG 0.5 0.895522
16 ARG PRO ARG PRO ASP ASP LEU GLU ILE 0.496296 0.882353
17 ARG PRO GLY ASN PHE PHE GLN SER ARG PRO 0.493151 0.873239
18 ALA MET ALA PRO ARG THR LEU LEU LEU 0.488722 0.873239
19 ARG GLU ARG SER PRO THR ARG 0.486957 0.893939
20 PRO SER ILE ASP ARG SER THR LYS PRO 0.485915 0.941176
21 PRO ALA ILE ILE ASN ARG PRO GLN ASN 0.48062 0.852941
22 ARG ARG ARG GLU ARG SER PRO THR ARG 0.477273 0.939394
23 PRO GLN ILE ILE ASN ARG PRO GLN ASN 0.477273 0.852941
24 VAL PRO PRO PRO ARG PRO PRO PRO PRO GLU 0.47541 0.892308
25 DPN PRO DAR DTH NH2 0.47541 0.850746
26 GLN ARG SER THR SEP THR PRO ASN VAL HIS 0.475177 0.824324
27 LEU ASP PRO ARG 0.474576 0.835821
28 PRO SER TYR SEP PRO THR SEP PRO SER 0.474576 0.75
29 SER TYR SER PRO THR SEP PRO SER 0.474576 0.763889
30 ARG ARG ALA SEP ALA PRO LEU PRO 0.474453 0.810811
31 ARG PRO GLY ASN PHE LEU GLN SER ARG PRO 0.474026 0.887324
32 LYS PRO VAL LEU ARG THR ALA 0.469697 0.910448
33 GLY GLU ARG THR ILE PRO ILE THR ARG GLU 0.466667 0.940298
34 VAL PRO LEU ARG PRO MET THR TYR 0.465753 0.84
35 LEU PRO PHE ASP ARG THR THR ILE MET 0.463576 0.851351
36 ASN ARG PRO ILE LEU SER LEU 0.458647 0.871429
37 ARG GLN PHE GLY PRO ASP PHE PRO THR ILE 0.458599 0.901408
38 ALA ASN SER ARG ALA PRO THR SER ILE ILE 0.457143 0.913043
39 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.456376 0.926471
40 ARG THR PRO SEP LEU PRO THR 0.455882 0.824324
41 SER LEU SER ARG THR PRO ALA ASP GLY ARG 0.454545 0.954545
42 ALA ASN SER ARG ALY PRO THR SER ILE ILE 0.452703 0.914286
43 ALA ASN SER ARG VAL PRO THR SER ILE ILE 0.451852 0.884058
44 GLY HIS ARG PRO NH2 0.45082 0.794118
45 PHE ASN ARG PRO VAL 0.449612 0.84058
46 SER PRO LYS ARG ILE ALA 0.446154 0.867647
47 SER ARG ASP HIS SER ARG THR PRO MET 0.444444 0.864865
48 DPN PRO DAR ILE NH2 0.44 0.768116
49 ACE ARG THR PRO SEP LEU PRO THR PIP 0.439716 0.805195
50 ARG PRO LYS ARG ILE ALA 0.438462 0.850746
51 THR LYS PRO ARG 0.4375 0.815385
52 ALA ASN SER ARG PHE PRO THR SER ILE ILE 0.437086 0.873239
53 ALA ASN SER ARG TRP PRO THR THR ARG LEU 0.433566 0.875
54 PRO LYS ARG PRO THR THR LEU ASN LEU PHE 0.433121 0.9
55 5JP PRO LYS ARG ILE ALA 0.432836 0.842857
56 VAL MET LEU PRO GLY ARG GLY VAL PRO 0.432432 0.802817
57 GLU THR LEU LEU ASP LEU ASP PHE ASP PRO 0.431818 0.797101
58 ILE SER PRO ARG THR LEU ASP ALA TRP 0.431138 0.864865
59 ALA ASN SER ARG TYR PRO THR SER ILE ILE 0.430464 0.863014
60 ASP VAL GLN THR GLY ARG ARG PRO TYR GLU 0.428571 0.914286
61 VAL MET ALA PRO ARG THR LEU PHE LEU 0.427632 0.849315
62 TYR PRO LYS ARG ILE ALA 0.425532 0.830986
63 SER HIS PRO ARG PRO ILE ARG VAL 0.424658 0.861111
64 THR PRO ARG ARG SER MLZ SER ALA 0.424242 0.885714
65 ALA PRO THR 0.424242 0.753846
66 ALA PRO THR MET PRO PRO PRO LEU PRO PRO 0.423077 0.788732
67 ASN ARG PRO VAL TYR ILE PRO ARG PRO PRO 0.42069 0.819444
68 LYS GLY PRO PRO LEU PRO ARG PRO ARG VAL 0.418605 0.835821
69 ARG VAL ALA SER PRO THR SER GLY VAL 0.417266 0.925373
70 ASP ARG VAL GLU LEU ASN ALA PRO ARG GLN 0.415493 0.882353
71 DPN PRO ARG 0.415254 0.776119
72 ARG PRO GLN VAL PRO LEU ARG PRO MET 0.413793 0.830986
73 PRO PRO ARG PRO ILE TYR ASN ARG ASN 0.413333 0.861111
74 LEU PRO GLU THR GLY 0.413223 0.80597
75 THR PRO GLN ASP LEU ASN THR MET LEU 0.412587 0.777778
76 PRO ARG ARG PRO VAL ILE MET ARG ARG 0.412587 0.777778
77 ARG PRO LYS PRO LEU VAL ASP PRO 0.410853 0.835821
78 GLN VAL PRO LEU ARG PRO MET THR TYR LYS 0.409639 0.853333
79 DMG PRO ARG ARG ARG SER ARG LYS PRO 0.409449 0.871429
80 SER PRO ARG LEU PRO LEU LEU GLU SER 0.409091 0.820895
81 ARG LEU TYR GLN ASN PRO THR THR TYR ILE 0.408805 0.84
82 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.408163 0.837838
83 ASP SER THR THR PRO ALA PRO THR NGA 0.407895 0.794521
84 LYS ALA PRO ARG ALY GLN LEU ALA THR LYS 0.406667 0.926471
85 ARG THR PRO SEP LEU PRO THR 49F 0.406452 0.794872
86 ACE ARG THR PRO SEP LEU PRO THR 60H 0.406452 0.794872
87 ACE GLN GLU ARG GLU VAL PRO CYS 0.405797 0.865672
88 DPN PRO DAR CYS NH2 0.404762 0.75
89 GLN PRO PRO VAL PRO PRO GLN ARG PRO MET 0.40411 0.830986
90 ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.402439 0.876712
91 GLY THR SER SER PRO SER ALA ASP 0.401575 0.833333
92 SER ASP ILE LEU PHE PRO ALA ASP SER 0.401408 0.760563
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5A2J; Ligand: ALA PRO ASP THR ARG PRO; Similar sites found: 152
This union binding pocket(no: 1) in the query (biounit: 5a2j.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2PAR TMP 0.01175 0.45223 None
2 2AE2 NAP 0.01785 0.4403 None
3 2AE2 PTO 0.01785 0.4403 None
4 4G1V FAD 0.005342 0.49872 1.63934
5 4BJZ P3A 0.01689 0.46073 1.63934
6 4BJZ FAD 0.01689 0.46073 1.63934
7 2BJF DXC 0.01082 0.45277 1.63934
8 3MB5 SAM 0.0166 0.4495 1.63934
9 3B20 NAD 0.0237 0.41827 1.63934
10 1Z4V DAN 0.03492 0.41799 1.63934
11 1D3V ABH 0.04265 0.40523 1.63934
12 2V9M CIT 0.01896 0.40353 1.63934
13 2PY4 DUP 0.03014 0.42771 1.72414
14 4L6C 0BT 0.01564 0.42296 1.9802
15 3L8W XAN 0.03105 0.4388 2.04918
16 1G41 ADP 0.04222 0.4301 2.04918
17 4HPP GLU 0.03653 0.41902 2.04918
18 2NZ2 CIR 0.04459 0.40552 2.04918
19 4M6T SAM 0.01531 0.44194 2.18579
20 3IOI 1GW 0.03838 0.41476 2.34899
21 1T26 GBD 0.02784 0.45713 2.45902
22 1T26 NAI 0.02784 0.45713 2.45902
23 4RNV FMN 0.002905 0.45058 2.45902
24 1RM0 NAI 0.02668 0.43522 2.45902
25 3O9P MHI 0.04902 0.43192 2.45902
26 2DTX BMA 0.04146 0.41985 2.45902
27 4RNV HBA 0.01784 0.41321 2.45902
28 3SIX GDP 0.01349 0.41291 2.45902
29 3RHZ UDP 0.02726 0.40596 2.45902
30 1C4U IH1 0.02989 0.40484 2.45902
31 1YBH FAD 0.01248 0.47437 2.71186
32 2Q37 3AL 0.004817 0.42329 2.76243
33 2Q6K ADN 0.01288 0.4679 2.82686
34 2R7K ACP 0.001925 0.52405 2.86885
35 2R7K AMZ 0.001925 0.52405 2.86885
36 1E8G FAD 0.01519 0.47228 2.86885
37 1E8G FCR 0.01465 0.47228 2.86885
38 3AIQ HBO 0.00689 0.46594 2.86885
39 1G7V PAI 0.008515 0.45636 2.86885
40 1P4C FMN 0.02095 0.45323 2.86885
41 1LVL FAD 0.01298 0.45036 2.86885
42 2AQJ FAD 0.02193 0.44845 2.86885
43 2AQJ TRP 0.02412 0.44552 2.86885
44 1XVV CCQ 0.03264 0.42541 2.86885
45 4WB7 ATP 0.02137 0.40439 2.86885
46 2ET1 GLV 0.03219 0.42482 2.98507
47 1RM4 NDP 0.01775 0.42602 3.27869
48 2WL9 MBD 0.03643 0.40738 3.27869
49 4M4Q 21A 0.01153 0.43267 3.3195
50 1F7K UMP 0.02007 0.41981 3.67647
51 4K5S FAD 0.003712 0.46859 3.68852
52 3O03 NAP 0.002632 0.46805 3.68852
53 2V6O FAD 0.01669 0.46213 3.68852
54 4FWE FAD 0.04849 0.41955 3.68852
55 4MOB COA 0.04096 0.41923 3.68852
56 3HPF GAE 0.04449 0.41448 3.68852
57 1GEE NAD 0.03953 0.41299 3.68852
58 2JE7 XMM 0.04844 0.40366 3.76569
59 2WPU KYT 0.02432 0.45595 3.77358
60 4EKV BTN 0.02887 0.42233 3.77358
61 1KY8 NAP 0.009228 0.48375 4.09836
62 4KS1 2H8 0.00335 0.48171 4.09836
63 2FH5 GTP 0.003998 0.44886 4.09836
64 2XZ3 MAL 0.02318 0.42267 4.09836
65 3VD8 MTT 0.01048 0.41327 4.09836
66 3NKT 1HN 0.04521 0.40521 4.09836
67 1B66 BIO 0.02442 0.41326 4.28571
68 2QQ0 ANP 0.04973 0.40777 4.34783
69 1R18 SAH 0.00513 0.44709 4.40529
70 1RYH GNP 0.007963 0.41754 4.4335
71 3RO7 TDR 0.02308 0.46226 4.5082
72 4KQL 1SG 0.01433 0.45994 4.5082
73 1DRV A3D 0.02099 0.44244 4.5082
74 1GRO ICT 0.02963 0.43354 4.5082
75 2AMV BIN 0.03308 0.43318 4.5082
76 2NLI FMN 0.04892 0.42783 4.5082
77 3HB5 NAP 0.04789 0.42364 4.5082
78 1YOE RIB 0.02446 0.42147 4.5082
79 2C31 TZD 0.007082 0.48243 4.91803
80 2C31 ADP 0.006913 0.48243 4.91803
81 1HV9 COA 0.03481 0.42935 4.91803
82 1HV9 UD1 0.03461 0.4283 4.91803
83 4KCF AKM 0.04421 0.42626 4.91803
84 3I3X U22 0.04898 0.42238 4.91803
85 4CMF PXG 0.005052 0.47744 5.32787
86 4MWV BCZ 0.01792 0.43733 5.32787
87 2NPX FAD 0.02624 0.42858 5.32787
88 2ZI8 SDT 0.04566 0.40743 5.32787
89 4J7H TRH 0.03196 0.40422 5.32787
90 1LO8 4CA 0.0404 0.43492 5.67376
91 1ZK4 AC0 0.002838 0.50756 5.7377
92 1ZK4 NAP 0.002838 0.50756 5.7377
93 1JA9 NDP 0.01267 0.46658 5.7377
94 4RJK TDL 0.03795 0.41278 5.7377
95 4AF0 MOA 0.04309 0.40366 5.7377
96 4DA6 GA2 0.01517 0.45455 5.92885
97 2W24 LYS 0.02854 0.41801 6
98 2VBQ BSJ 0.006451 0.45734 6.06061
99 1X1T NAD 0.003807 0.49687 6.14754
100 3K37 BCZ 0.009824 0.47615 6.14754
101 4W6Z 8ID 0.04481 0.41528 6.14754
102 3K9W 4PS 0.03702 0.45038 6.41711
103 3K9W ADE 0.03702 0.45038 6.41711
104 1CX9 NHP 0.005922 0.48961 6.55738
105 2YYJ 4HP 0.007961 0.48343 6.55738
106 2YYJ FAD 0.007961 0.48343 6.55738
107 4B63 ORN 0.01544 0.48328 6.55738
108 4B63 FAD 0.01544 0.48328 6.55738
109 4B63 NAP 0.02559 0.4709 6.55738
110 1J2Z SOG 0.0128 0.45156 6.55738
111 3CKZ ZMR 0.02664 0.43191 6.55738
112 1RSD PSB 0.02773 0.47508 6.61157
113 1S8F GDP 0.001422 0.48157 6.77966
114 1R37 NAD 0.04913 0.41119 6.91643
115 1GSA ADP 0.03366 0.43129 6.96721
116 1FIQ FAD 0.04786 0.4118 6.96721
117 4TMK T5A 0.008574 0.49208 7.04225
118 1WKL ATP 0.01813 0.44817 7.29927
119 4OYA 1VE 0.02295 0.46366 7.37705
120 4QN7 G39 0.01133 0.44571 7.37705
121 1P72 ADP 0.004442 0.46206 7.78689
122 4PVV HO4 0.04219 0.41855 7.78689
123 1D7O TCL 0.005293 0.49344 8.19672
124 1D7O NAD 0.005293 0.49344 8.19672
125 1K97 ASP 0.03601 0.44622 8.19672
126 1K97 CIR 0.03601 0.44622 8.19672
127 1Q7E MET 0.01412 0.43108 8.19672
128 2NVK FAD 0.03524 0.4254 8.19672
129 3SJ7 NDP 0.03372 0.41427 8.19672
130 3ZZL TRP 0.006239 0.46349 8.57143
131 2BH9 NAP 0.01083 0.42181 8.60656
132 4NE2 ADP 0.03935 0.41526 8.60656
133 4NE2 SH2 0.043 0.41526 8.60656
134 1O6B ADP 0.03796 0.42613 8.87574
135 2CCV A2G 0.001483 0.47904 8.91089
136 1JSH SIA GAL 0.01552 0.42312 9.01639
137 3C2O NTM 0.007912 0.48757 9.42623
138 3D2M COA 0.03191 0.45535 9.83607
139 2B4Q NAP 0.03172 0.41683 10.2459
140 2D2I NAP 0.03117 0.41083 10.6557
141 2FWP CIT 0.03291 0.41715 10.929
142 1SAY PYR 0.003091 0.52022 11.0656
143 4HZX G39 0.01554 0.44255 14.7541
144 3CH5 GDP 0.04135 0.41413 15.3846
145 1VL8 NAP 0.03908 0.41542 15.5738
146 1R27 MGD 0.02369 0.42994 16.3934
147 1UQX MMA 0.04308 0.40366 23.0089
148 1CT8 TAA 0.01465 0.40238 35.9091
149 1C1E ENH 0.003525 0.42955 36.0731
150 1MH5 HAL 0.0009235 0.47584 36.087
151 1D6V HOP 0.01273 0.41412 38.4615
152 1LO0 BC1 0.0407 0.40056 42.7273
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