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Receptor
PDB id Resolution Class Description Source Keywords
1Q3P 2.25 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF THE SHANK PDZ-LIGAND COMPLEX REVEALS A CLASS I PDZ INTERACTION AND A NOVEL PDZ-PDZ DIMERIZATION RATTUS NORVEGICUS SHANK PDZ GKAP CRYSTAL STRUCTURE PEPTIDE BINDING PROTEIN
Ref.: CRYSTAL STRUCTURE OF THE SHANK PDZ-LIGAND COMPLEX REVEALS A CLASS I PDZ INTERACTION AND A NOVEL PDZ-PDZ DIMERIZATION J.BIOL.CHEM. V. 278 48099 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLU ALA GLN THR ARG LEU C:1;
D:1;
Valid;
Valid;
none;
none;
submit data
716.794 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1Q3P 2.25 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF THE SHANK PDZ-LIGAND COMPLEX REVEALS A CLASS I PDZ INTERACTION AND A NOVEL PDZ-PDZ DIMERIZATION RATTUS NORVEGICUS SHANK PDZ GKAP CRYSTAL STRUCTURE PEPTIDE BINDING PROTEIN
Ref.: CRYSTAL STRUCTURE OF THE SHANK PDZ-LIGAND COMPLEX REVEALS A CLASS I PDZ INTERACTION AND A NOVEL PDZ-PDZ DIMERIZATION J.BIOL.CHEM. V. 278 48099 2003
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 3QJM - ASP GLU THR ASN LEU n/a n/a
2 1Q3P - GLU ALA GLN THR ARG LEU n/a n/a
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 families.
1 5OVV Kd = 33 uM ACE ILE GLU SER THR GLU ILE n/a n/a
2 3QJM - ASP GLU THR ASN LEU n/a n/a
3 1Q3P - GLU ALA GLN THR ARG LEU n/a n/a
4 5OVC Kd = 1.1 uM ACE GLU ALA GLN THR ARG LEU n/a n/a
5 6EXJ Kd = 47 uM ACE ASP LEU GLN THR SER ILE n/a n/a
6 5OVP Kd = 9.1 uM ACE GLN LEU VAL THR SER LEU n/a n/a
7 3O5N Ki = 17.2 uM BR0 C14 H12 N2 O6 c1cc(c2c(c....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 174 families.
1 5EMB - GLN GLU GLU TRP SEP THR VAL MET n/a n/a
2 5ELQ Kd = 2 uM ARG GLU ASP GLN GLU THR ALA VAL n/a n/a
3 5EMA Kd = 5.9 uM PRO ASP ASP ILE SEP THR VAL VAL n/a n/a
4 5EM9 Kd = 2.7 uM PRO GLU SEP LEU GLU SER CYS PHE n/a n/a
5 5OVV Kd = 33 uM ACE ILE GLU SER THR GLU ILE n/a n/a
6 1RZX Kd = 80 uM ACE VAL LYS GLU SER LEU VAL n/a n/a
7 5I7Z - LEU PRO PRO GLU GLU ARG LEU ILE n/a n/a
8 1Q3P - GLU ALA GLN THR ARG LEU n/a n/a
9 6EXJ Kd = 47 uM ACE ASP LEU GLN THR SER ILE n/a n/a
10 5OVP Kd = 9.1 uM ACE GLN LEU VAL THR SER LEU n/a n/a
11 3O5N Ki = 17.2 uM BR0 C14 H12 N2 O6 c1cc(c2c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLU ALA GLN THR ARG LEU; Similar ligands found: 152
No: Ligand ECFP6 Tc MDL keys Tc
1 GLU ALA GLN THR ARG LEU 1 1
2 ACE GLU ALA GLN THR ARG LEU 0.783505 0.980392
3 THR ARG ARG GLU THR GLN LEU 0.739583 0.961538
4 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.673077 0.961538
5 ARG ARG ARG GLU THR GLN VAL 0.62 0.942308
6 ALA ARG THR M3L GLN THR ALA ARG 0.611111 0.806452
7 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.580357 0.980392
8 ARG ASP ARG ALA ALA LYS LEU 0.57 0.846154
9 GLU ALA THR GLN LEU MET ASN 0.568807 0.777778
10 SER GLU ILE GLU PHE ALA ARG LEU 0.565574 0.890909
11 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.564103 0.806452
12 ALA ARG THR MLY GLN THR ALA ARG TYR 0.544715 0.757576
13 ALA ARG THR MLY GLN 0.542056 0.847458
14 ALA ARG THR GLU LEU TYR ARG SER LEU 0.540323 0.847458
15 SER SER ILE GLU PHE ALA ARG LEU 0.539683 0.875
16 ALA ARG THR LYS GLN THR ALA ARG LYS 0.535088 0.886792
17 GLN THR ALA ARG M3L SER 0.534483 0.777778
18 ALA ALA LEU THR ARG ALA 0.528302 0.96
19 SER ASP TYR GLN ARG LEU 0.526316 0.857143
20 ARG GLU ASP GLN GLU THR ALA VAL 0.523364 0.784314
21 SAC ARG GLY THR GLN THR GLU 0.521739 0.888889
22 GLU THR VAL ARG PHE GLN SER ASP 0.519685 0.907407
23 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.516949 0.842105
24 ILE GLN GLN SER ILE GLU ARG ILE 0.508772 0.90566
25 GLN ARG ALA THR LYS MET NH2 0.508475 0.857143
26 HIS GLU GLU LEU ALA LYS LEU 0.504951 0.764706
27 ACE GLN THR ALA ARG PRK SER THR 0.504202 0.839286
28 MET ABA LEU ARG MET THR ALA VAL MET 0.504065 0.875
29 GLN THR ALA ARG M3L SER THR GLY 0.504065 0.777778
30 MET CYS LEU ARG MET THR ALA VAL MET 0.504 0.875
31 ACE CSO ARG ALA THR LYS MET LEU 0.5 0.78125
32 ALA ARG THR ALY GLN THR ALA 0.5 0.854545
33 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.5 0.790323
34 ACE GLN THR ALA ARG BTK SER THR 0.5 0.872727
35 ALA ARG THR M3L GLN THR ALA 0.5 0.790323
36 ALA ARG THR M3L GLN THR ALA ARG LYS 0.495575 0.790323
37 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.495575 0.790323
38 MET CYS LEU ARG NLE THR ALA VAL MET 0.492188 0.859649
39 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.491228 0.816667
40 ALA ARG THR MLY GLN THR ALA 0.491228 0.816667
41 GLU LEU LYS TPO GLU ARG TYR 0.488722 0.742424
42 GLU GLU TYR LEU GLN ALA PHE THR TYR 0.488372 0.706897
43 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.488189 0.790323
44 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.487805 0.833333
45 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.487805 0.833333
46 ALA ARG THR MLY GLN THR ALA ARG LYS 0.486957 0.830508
47 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.486957 0.857143
48 ALA ASN SER ARG TRP GLN ASP THR ARG LEU 0.485915 0.769231
49 ARG ARG ILE TYR ASP LEU ILE GLU LEU 0.484848 0.813559
50 ACE ALA ARG THR GLU VAL TYR NH2 0.483607 0.875
51 THR ILE MET MET GLN ARG GLY 0.482759 0.859649
52 LEU GLU LYS ALA ARG GLY SER THR TYR 0.482269 0.819672
53 GLU ARG GLY MET THR 0.482143 0.854545
54 ACE GLN THR ALA ARG KCR SER THR 0.475806 0.854545
55 ALA GLN THR ALA ARG ALY SER THR 0.47541 0.839286
56 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.474453 0.790323
57 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.472222 0.921569
58 LEU LYS THR LYS LEU LEU 0.471154 0.826923
59 GLU GLU ASN LEU LEU ASP PHE VAL ARG PHE 0.470149 0.810345
60 VAL ALA ARG SER 0.47 0.882353
61 ALA ARG THR LYS GLN THR ALA ARG 0.468468 0.903846
62 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.46729 0.901961
63 LYS THR LYS LEU LEU 0.466019 0.826923
64 ARG GLU ALA ALA 0.465347 0.86
65 ILE PRO LEU THR GLU GLU ALA GLU LEU 0.464 0.661538
66 ALA ASN SER ARG VAL GLN ASP SER ILE ILE 0.464 0.890909
67 ASN PRO ARG ALA MET GLN ALA LEU LEU 0.462687 0.681159
68 ASN ARG LEU MET LEU THR GLY 0.461538 0.892857
69 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.458333 0.774194
70 ALA ARG 9AT 0.457447 0.92
71 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.45614 0.830508
72 ARG ARG ALA ALA 0.454545 0.823529
73 GLU ALA ALA GLY ILE GLY ILE LEU THR VAL 0.454545 0.826923
74 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.453782 0.842105
75 ARG ARG ALA THR LYS MET NH2 0.453782 0.824561
76 ILE LYS LEU GLU THR LYS LYS THR LYS LEU 0.45283 0.8
77 ARG VAL ALA GLN LEU GLU GLN VAL TYR ILE 0.451852 0.824561
78 VAL LEU ARG ASP ASP LEU LEU GLU ALA 0.451327 0.884615
79 SER GLU LEU GLU ILE LYS ARG TYR 0.451128 0.833333
80 GLU LEU LYS ARG LYS MET ILE TYR MET 0.446043 0.746032
81 MET ALA ARG 0.445545 0.796296
82 MET ARG THR GLY ASN ALA XSN 0.444444 0.844828
83 GLY GLU ARG THR ILE PRO ILE THR ARG GLU 0.444444 0.742424
84 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.443609 0.807018
85 GLU LEU ALA ALA ILE GLY ILE LEU THR VAL 0.442623 0.843137
86 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.442478 0.888889
87 HIS GLY ALA ALA ARG ALA GLU VAL HIS LEU 0.440678 0.862745
88 LEU ALA SER LEU GLU SER GLN SER 0.440367 0.807692
89 ARG GLN ALA SEP LEU SER ILE SER VAL 0.440298 0.816667
90 ALA MET ALA PRO ARG THR LEU LEU LEU 0.440298 0.710145
91 SER SER THR ARG GLY ILE SER GLN LEU TRP 0.44 0.769231
92 ALA GLN ASP ILE TYR ARG ALA SER TYR 0.439716 0.803279
93 ASP ALA GLU PHE ARG HIS ASP 0.439024 0.830189
94 LYS LEU VAL GLN LEU LEU THR THR THR 0.438596 0.846154
95 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.437956 0.786885
96 ACE ALA ARG THR LYS GLN 0.4375 0.884615
97 ARG GLN PRO ALA LYS ALA PRO LEU LEU 0.434783 0.671642
98 VAL ARG SER ARG ARG ABA LEU ARG LEU 0.434783 0.888889
99 ALA GLN PHE SER ALA SER ALA SER ARG 0.434426 0.854545
100 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.434343 0.84
101 ASN ALA LEU LEU ARG TYR LEU LEU ASP 0.433071 0.844828
102 GLU LEU ARG ARG LYS MET MET TYR MET 0.431818 0.746032
103 VAL PRO LEU THR GLU ASP ALA GLU LEU 0.430769 0.671875
104 GLU LEU ASN ARG LYS MET ILE TYR MET 0.428571 0.765625
105 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.428571 0.857143
106 THR PHE GLN ALA PSA LEU ARG GLU 0.427586 0.862069
107 ASN SER THR LEU GLN 0.425926 0.773585
108 GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU 0.425532 0.634921
109 SER GLN LEU LYS ASN ASN ALA LYS GLU ILE 0.424 0.754386
110 PHQ GLN THR ALA ARG LYS NH2 FOA 0.422535 0.738462
111 ASN ARG LEU LEU LEU THR GLY 0.422018 0.960784
112 ALA THR VAL ARG THR TYR SER CYS 0.421875 0.813559
113 ALA PRO ALA LEU ARG VAL VAL LYS 0.421053 0.846154
114 GLU LEU ARG SER ARG TYR TRP ALA ILE 0.421053 0.735294
115 LEU PRO PHE GLU ARG ALA THR ILE MET 0.420382 0.704225
116 SER ARG TYR TRP ALA ILE ARG THR ARG 0.42 0.705882
117 GLU LEU ALA GLY ILE GLY ILE ALA THR VAL 0.419355 0.826923
118 ACE GLN LEU VAL THR SER LEU 0.418182 0.792453
119 ALA ARG LYS LEU ASP 0.418182 0.884615
120 LEU PRO PHE GLU ARG ALA THR VAL MET 0.416667 0.714286
121 PTR LEU ARG VAL ALA 0.416 0.703125
122 PHE LEU ARG GLY ARG ALA TYR VAL LEU 0.415493 0.783333
123 ALA 2MR THR MLY GLN THR ALA ALA 0.415254 0.816667
124 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.414966 0.714286
125 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.414815 0.777778
126 LYS SER LEU LEU GLN GLN LEU LEU THR GLU 0.414634 0.814815
127 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.414634 0.849057
128 LYS GLN THR ALA ARG M3L SER THR GLY 0.414634 0.777778
129 GLU LEU ALA GLY ILE GLY ILE LEU THR VAL 0.414634 0.826923
130 LYS PRO VAL LEU ARG THR ALA 0.411765 0.765625
131 ASP LEU THR ARG PRO 0.41129 0.78125
132 GLU ASP LEU 0.410526 0.72
133 GLU THR LEU LEU ASP LEU ASP PHE LEU GLU 0.409091 0.769231
134 2NC 0.408 0.872727
135 ARG GLY TYR VAL TYR GLN GLY LEU 0.407407 0.79661
136 MET CYS PRO ARG MET THR ALA VAL MET 0.406897 0.710145
137 ARG ILE ILE PRO ARG HIS LEU GLN LEU 0.406667 0.642857
138 ALA ASN SER ARG TRP GLN THR SER ILE ILE 0.406667 0.753846
139 GLN ILE LYS VAL ARG VAL ASP MET VAL 0.406015 0.807018
140 GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG 0.405594 0.79661
141 ASN ARG LEU ILE LEU THR GLY 0.405172 0.865385
142 ALA SER ASN GLU ASN ALA GLU THR MET 0.404959 0.724138
143 ARG GLN ALA SEP ILE GLU LEU PRO SER MET 0.404908 0.636364
144 ACE GLN GLU ARG GLU VAL PRO CYS 0.40458 0.666667
145 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.404412 0.783333
146 ALA ASN SER ARG TRP PRO THR THR ARG LEU 0.403846 0.684932
147 GLU ALY ARG 0.401786 0.777778
148 ACE ASP LEU GLN THR SER ILE 0.401709 0.777778
149 ARG GLY TYR LEU TYR GLN GLY LEU 0.401515 0.79661
150 ASP ALA GLU PHE ARG HIS ASP SER 0.40146 0.693548
151 PHE TYR ARG ALA LEU MET 0.4 0.741935
152 ASP ALA ASP GLU TYR LEU 0.4 0.666667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1Q3P; Ligand: GLU ALA GLN THR ARG LEU; Similar sites found with APoc: 56
This union binding pocket(no: 1) in the query (biounit: 1q3p.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4XMF HSM None
2 6GNO XDI None
3 3R9V DXC None
4 2BVE PH5 None
5 2D3Y DU None
6 1Z0N BCD None
7 5XVG 8FX None
8 5WHU SIA GAL None
9 4G0P U5P None
10 4XPL ACO None
11 3PE2 E1B 2.75229
12 1NE7 16G 2.75229
13 3I7V B4P 3.66972
14 5CCM SAM 3.66972
15 5CCM 4ZX 3.66972
16 2Z9I GLY ALA THR VAL 4.58716
17 2NZ5 226 4.58716
18 4CS4 ANP 4.58716
19 4CS4 AXZ 4.58716
20 3HAD NAD 4.58716
21 4Y8D 49J 4.58716
22 3SJK LYS PRO VAL LEU ARG THR ALA 5.26316
23 3B99 U51 5.50459
24 4UXH T5A 5.50459
25 1S4M LUM 6.42202
26 2XOC ADP 6.42202
27 5FPE 3TR 6.42202
28 2W5P CL8 6.42202
29 5L83 ASP TRP GLU ILE VAL 7.33945
30 3U7Q HCA 7.33945
31 5KJK 6T1 7.33945
32 5KJK SAM 7.33945
33 1ELI PYC 7.33945
34 2VNF ALA ARG THR M3L GLN THR ALA ARG LYS SER 8.33333
35 6C8X BVR 9.09091
36 2Z3U CRR 9.17431
37 4L3L 5FI 9.17431
38 1V0C ACO 9.17431
39 1V0C KNC 9.17431
40 5YW5 ADE 9.17431
41 2B6N ALA PRO THR 10.0917
42 1FFU CDP 11.0092
43 3E70 GDP 11.0092
44 4YG6 GAL NAG 12.844
45 3F5A SIA GAL NAG 13.7615
46 5T63 ALA ALA ALA ALA 13.7615
47 3LTW HLZ 15.5963
48 1PVC ILE SER GLU VAL 18.3486
49 4C2C ALA VAL PRO ALA 22.0183
50 4C2C ALA ALA ALA 22.0183
51 1L6O SER LEU LYS LEU MET THR THR VAL 24.2105
52 4B2H C3F 24.3243
53 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 25.6881
54 1TZD ADP 25.6881
55 1MFG GLU TYR LEU GLY LEU ASP VAL PRO VAL 26.3158
56 5VWK PRO ALA TRP ASP GLU THR ASN LEU 42.2018
Pocket No.: 2; Query (leader) PDB : 1Q3P; Ligand: GLU ALA GLN THR ARG LEU; Similar sites found with APoc: 34
This union binding pocket(no: 2) in the query (biounit: 1q3p.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4AF5 CIT None
2 4KS7 X4Z None
3 6BMN PAP 1.83486
4 5LYH 7B8 2.75229
5 1FIW PBZ 3.66972
6 4MSG 2C6 3.66972
7 4D3S BOG 4.58716
8 4LRL TTP 4.58716
9 4BUY F37 4.58716
10 4FC7 NAP 5.50459
11 4FC7 COA 5.50459
12 1RC0 KT5 6.42202
13 4LXQ FON 6.42202
14 4LXQ TYD 6.42202
15 4CQE CQE 6.42202
16 1S17 GNR 7.33945
17 3M2W L8I 7.33945
18 3RZ3 U94 8.25688
19 4LO6 SIA GAL 9.17431
20 5BVE 4VG 9.17431
21 4QMN DB8 9.17431
22 4CFU 2WC 10.0917
23 4OMJ 2TX 11.0092
24 5GVL GI8 11.9266
25 5GVL PLG 11.9266
26 3WGT QSC 12.844
27 1W4R TTP 12.844
28 5LWY OLB 13.0841
29 3AFN NAP 13.7615
30 5W4W 9WG 16.5138
31 5NDF UDP 16.5138
32 2CYE COA 16.5138
33 4UYW H1S 18.3486
34 1E7S NAP 20.1835
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