Receptor
PDB id Resolution Class Description Source Keywords
5TB5 2 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF FULL-LENGTH FARNESYLATED AND METHYLATED COMPLEX WITH PDE-DELTA (CRYSTAL FORM I - WITH PARTIALLY DISH YPERVARIABLE REGION) HOMO SAPIENS KRAS4B PDEDELTA PDE6DELTA RAS KRAS ONCOPROTEIN
Ref.: STRUCTURAL BASIS OF RECOGNITION OF FARNESYLATED AND METHYLATED KRAS4B BY PDE DELTA. PROC.NATL.ACAD.SCI.USA V. 113 E6766 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:201;
D:201;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GDP C:202;
A:202;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
FAR C:201;
A:201;
Invalid;
Invalid;
none;
none;
submit data
206.367 C15 H26 CC=C(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TB5 2 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF FULL-LENGTH FARNESYLATED AND METHYLATED COMPLEX WITH PDE-DELTA (CRYSTAL FORM I - WITH PARTIALLY DISH YPERVARIABLE REGION) HOMO SAPIENS KRAS4B PDEDELTA PDE6DELTA RAS KRAS ONCOPROTEIN
Ref.: STRUCTURAL BASIS OF RECOGNITION OF FARNESYLATED AND METHYLATED KRAS4B BY PDE DELTA. PROC.NATL.ACAD.SCI.USA V. 113 E6766 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 5TB5 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5TB5 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 5TB5 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 161
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 9GM 0.839506 0.973684
6 GNP 0.839506 0.973684
7 G 0.828947 0.986486
8 5GP 0.828947 0.986486
9 G1R 0.82716 0.986667
10 GCP 0.82716 0.973684
11 GSP 0.817073 0.948718
12 GAV 0.797619 0.961039
13 GMV 0.792683 0.973684
14 G2P 0.77381 0.961039
15 G2R 0.770115 0.961039
16 GP2 0.756098 0.961039
17 GDC 0.747253 0.961039
18 GKE 0.747253 0.961039
19 GDD 0.747253 0.961039
20 GPG 0.741573 0.961039
21 G3D 0.732558 0.986486
22 ALF 5GP 0.729412 0.888889
23 Y9Z 0.728261 0.902439
24 G5P 0.723404 0.973684
25 GFB 0.72043 0.961039
26 GTG 0.72043 0.936709
27 GDR 0.72043 0.961039
28 G4P 0.715909 0.986486
29 G3A 0.712766 0.973684
30 6CK 0.712766 0.936709
31 GDP AF3 0.7 0.888889
32 ALF GDP 0.7 0.888889
33 GDP ALF 0.7 0.888889
34 YGP 0.698925 0.901235
35 GKD 0.697917 0.961039
36 JB2 0.697917 0.961039
37 GDX 0.690722 0.973684
38 GPD 0.690722 0.925
39 GMP 0.684211 0.88
40 0O2 0.666667 0.986486
41 JB3 0.656863 0.948718
42 NGD 0.650485 0.961039
43 DGI 0.636364 0.923077
44 GDP 7MG 0.636364 0.911392
45 U2G 0.634615 0.936709
46 GPX 0.634409 0.946667
47 G G 0.632653 0.948052
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 CG2 0.622642 0.936709
52 FEG 0.619048 0.879518
53 MGD 0.614679 0.891566
54 ZGP 0.613208 0.869048
55 GH3 0.612903 0.973333
56 3GP 0.611765 0.946667
57 MD1 0.607143 0.891566
58 PGD 0.59292 0.925
59 DGT 0.591398 0.923077
60 BGO 0.588785 0.924051
61 TPG 0.582609 0.840909
62 DBG 0.582609 0.948718
63 2GP 0.574713 0.96
64 FE9 0.570175 0.776596
65 GCP G 0.56 0.921053
66 A G 0.553571 0.935065
67 G A A A 0.553571 0.923077
68 MGP 0.553191 0.961039
69 U A G G 0.548673 0.935065
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 G1R G1R 0.542373 0.924051
73 P2G 0.527473 0.883117
74 PGD O 0.525 0.850575
75 ADP 0.522222 0.92
76 R5I 0.520833 0.946667
77 R7I 0.520833 0.946667
78 GGM 0.517544 0.901235
79 DGP 0.516484 0.910256
80 DG 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G U 0.513274 0.9
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 AKW 0.504425 0.890244
86 G C 0.504348 0.9
87 GPC 0.491525 0.879518
88 G7M 0.483871 0.948052
89 6AD 0.479592 0.841463
90 ATP 0.473684 0.92
91 HEJ 0.473684 0.92
92 G2Q 0.471154 0.961039
93 5FA 0.46875 0.92
94 AQP 0.46875 0.92
95 GTA 0.468468 0.936709
96 7DD 0.468085 0.906667
97 G G G RPC 0.466102 0.875
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 B4P 0.457447 0.894737
102 AP5 0.457447 0.894737
103 A2D 0.456522 0.894737
104 6YZ 0.455446 0.896104
105 G G G C 0.455285 0.9125
106 5GP 5GP 0.454545 0.883117
107 ANP 0.454545 0.896104
108 ACQ 0.454545 0.896104
109 AT4 0.452632 0.884615
110 A G C C 0.451613 0.911392
111 APC G U 0.45082 0.886076
112 PRT 0.449541 0.959459
113 G U34 0.449153 0.888889
114 DG DG 0.448598 0.865854
115 ITT 0.447917 0.868421
116 BA3 0.446809 0.894737
117 C2E 0.444444 0.921053
118 PCG 0.444444 0.933333
119 35G 0.444444 0.933333
120 MGO 0.441176 0.864198
121 AN2 0.4375 0.907895
122 G C C C 0.4375 0.924051
123 M33 0.43299 0.883117
124 UCG 0.429688 0.911392
125 A G U 0.42963 0.888889
126 ACP 0.428571 0.896104
127 MGQ 0.424528 0.935897
128 AR6 0.424242 0.894737
129 7DT 0.424242 0.906667
130 APR 0.424242 0.894737
131 93A 0.42268 0.833333
132 A4P 0.420168 0.869048
133 G8D 0.42 0.875
134 AD9 0.42 0.896104
135 SAP 0.42 0.873418
136 AGS 0.42 0.873418
137 CA0 0.418367 0.896104
138 ATF 0.417476 0.884615
139 AGO 0.414634 0.888889
140 A G U U 0.414286 0.888889
141 NIA 0.413043 0.82716
142 MGV 0.412844 0.890244
143 TAT 0.411765 0.884615
144 T99 0.411765 0.884615
145 ADQ 0.411215 0.871795
146 A1R 0.411215 0.839506
147 RGT 0.410714 0.909091
148 CGP 0.409836 0.86747
149 C1Z 0.409091 0.986486
150 A 0.408602 0.893333
151 AMP 0.408602 0.893333
152 UP5 0.40678 0.873418
153 AMZ 0.406593 0.918919
154 C2R 0.406593 0.906667
155 JBT 0.405882 0.778947
156 A22 0.40566 0.907895
157 25L 0.405405 0.907895
158 ADX 0.40404 0.809524
159 8OD 0.401961 0.946667
160 50T 0.4 0.883117
161 4TC 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TB5; Ligand: GDP; Similar sites found with APoc: 146
This union binding pocket(no: 1) in the query (biounit: 5tb5.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 1YRB GDP 4.86486
2 3WY9 GDP 4.86486
3 3WYA GDP 4.86486
4 3MD0 GDP 5.33333
5 6G14 G4P 6.48649
6 4RD0 GDP 7.33333
7 2RCN GDP 8
8 6AU6 GDP 8.10811
9 3EC1 GDP 8.10811
10 1KK1 GNP 8.66667
11 1SKQ GDP 9.18919
12 5W7Q GDP 9.33333
13 5W75 GDP 10.6667
14 2C78 GNP 10.8108
15 4NON GDP 10.8108
16 4J0Q GDP 11.3514
17 2XTZ GSP 13.3333
18 3U6B GDP 14
19 2HCJ GDP 14
20 2BVN GNP 14
21 1D8T GDP 14
22 4P3Y GDP 14
23 5JBQ GDP 14
24 4G5G GDP 14
25 3U6K GDP 14
26 4PC3 GDP 14
27 1MKY GDP 14.5946
28 5EE5 GTP 16.9591
29 2X77 GDP 17.2973
30 3PCR GTP 17.9012
31 5CK5 GDP 20
32 5HCN GCP 23.2432
33 5FG3 GDP 23.2432
34 4B47 GDP 25.4054
35 5YT0 GDP 25.9459
36 4M9Q GNP 25.9459
37 2W83 GTP 25.9459
38 2A5F GTP 26.4865
39 3DOE GTP 27.5676
40 4DCT GDP 28.1081
41 1J2J GTP 29.1892
42 2J59 GTP 29.1892
43 1O3Y GTP 29.1892
44 1MR3 G3D 29.1892
45 1ZD9 GDP 30.2703
46 4YLG GDP 30.2703
47 5KUT GDP 30.2703
48 1ZJ6 G3D 30.8108
49 1YZG GDP 31.2849
50 1R4A GNP 33.3333
51 2QN6 GDP 33.3333
52 4ZI2 GNP 37.2973
53 1FZQ GDP 37.2973
54 2GJ8 ALF GDP 37.8378
55 1M7B GTP 41.0811
56 1SVI GDP 42.1622
57 3GJ7 GDP 43.2432
58 5OEC GDP 43.2432
59 3GJ5 GDP 43.2432
60 3M1I GTP 43.2432
61 3WYF GTP 43.2432
62 3WYG GTP 43.2432
63 3GJ8 GDP 43.2432
64 3GJ4 GDP 43.2432
65 5BXQ GDP 43.7838
66 5UWQ GNP 43.7838
67 3RAB GNP 43.7838
68 5UWJ GNP 43.7838
69 5UWP GNP 43.7838
70 5UWU GNP 43.7838
71 5UWO GNP 43.7838
72 4HAT GNP 43.7838
73 5UWW GNP 43.7838
74 6CIT GNP 43.7838
75 5UWR GNP 43.7838
76 5UWI GNP 43.7838
77 5UWS GNP 43.7838
78 5DHF GNP 43.7838
79 5UWH GNP 43.7838
80 4DKX GDP 43.7838
81 5UWT GNP 43.7838
82 5LEF GTP 43.7838
83 1WA5 GTP 43.7838
84 3GJ0 GDP 43.7838
85 3GJ3 GDP 43.7838
86 3CH5 GDP 43.7838
87 3REF GDP 43.7838
88 2EW1 GNP 44.3243
89 1Z0J GTP 44.8649
90 2W2X GSP 44.8649
91 1YVD GNP 45.4054
92 1DS6 GDP 45.4054
93 5UPK GNP 45.4054
94 1A4R GDP 45.4054
95 1A4R GNH 45.4054
96 1NF3 GNP 45.4054
97 3E5H GNP 45.9459
98 4DID GDP 45.9459
99 2NGR GDP 45.9459
100 4YC7 GNP 45.9459
101 2WKQ GTP 45.9459
102 2WMO GTP 45.9459
103 1GRN GDP 45.9459
104 1E96 GTP 46.4865
105 1I4D GDP 47.027
106 2FJU GSP 47.027
107 3Q72 GNP 47.5676
108 3SBD GNP 47.5676
109 1CXZ GSP 47.5676
110 4D0G GTP 47.5676
111 1KMQ GNP 47.8261
112 1Z0A GDP 48.1081
113 1Z0F GDP 48.1081
114 1Z0K GTP 48.1081
115 3LXR GDP 48.1081
116 2G77 GDP 48.1081
117 1MH1 GNP 48.1081
118 4D0N GDP 48.1081
119 4XSH GSP 48.1081
120 6BCB GSP 48.1081
121 6BCA GSP 48.1081
122 1G4U GDP 48.1081
123 1TX4 ALF GDP 48.1081
124 6BC0 GSP 48.1081
125 1YZQ GNP 48.2353
126 2BME GNP 48.6486
127 2D7C GTP 48.6486
128 1Z2A GDP 48.6486
129 2F9L GDP 48.6486
130 2GCN GDP 48.6486
131 1RYH GNP 48.6486
132 2GCO GNP 48.6486
133 4XOI GTP 48.8889
134 1Z06 GNP 49.1892
135 2A5J GDP 49.1892
136 5Z2M GTP 49.1892
137 3BC1 GNP 49.1892
138 1OIX GDP 49.1892
139 3Q85 GNP 49.1892
140 5XC5 GTP 49.4318
141 1OIV GDP 49.7297
142 2HV8 GTP 49.7297
143 4C4P GNP 49.7297
144 3RWO GDP 49.7297
145 1KY3 GDP 49.7297
146 4U5X GNP 49.7297
Pocket No.: 2; Query (leader) PDB : 5TB5; Ligand: GDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5tb5.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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