Receptor
PDB id Resolution Class Description Source Keywords
3D6T 2.43 Å EC: 2.7.11.1 STRUCTURE OF THE ROC DOMAIN FROM THE PARKINSON'S DISEASE-ASS LEUCINE-RICH REPEAT KINASE 2 REVEALS A DIMERIC GTPASE HOMO SAPIENS PARKINSON-prime S DISEASE LRRK2 ROC ROCO GTPASE KINASE ATP-BDISEASE MUTATION GTP-BINDING GTPASE ACTIVATION LEUCINE-RREPEAT MEMBRANE NUCLEOTIDE-BINDING PARKINSON DISEASE SERINE/THREONINE-PROTEIN KINASE TRANSFERASE
Ref.: STRUCTURE OF THE ROC DOMAIN FROM THE PARKINSON'S DISEASE-ASSOCIATED LEUCINE-RICH REPEAT KINASE 2 REV DIMERIC GTPASE PROC.NATL.ACAD.SCI.USA V. 105 1499 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP B:1;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG B:2;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2ZEJ 2 Å EC: 2.7.11.1 STRUCTURE OF THE ROC DOMAIN FROM THE PARKINSON'S DISEASE-ASS LEUCINE-RICH REPEAT KINASE 2 REVEALS A DIMERIC GTPASE HOMO SAPIENS PARKINSON-prime S DISEASE LRRK2 ROC GTPASE ROCO KINASE ATP-BDISEASE MUTATION GTP-BINDING GTPASE ACTIVATION LEUCINE-RREPEAT MEMBRANE NUCLEOTIDE-BINDING PARKINSON DISEASE SERINE/THREONINE-PROTEIN KINASE TRANSFERASE
Ref.: STRUCTURE OF THE ROC DOMAIN FROM THE PARKINSON'S DISEASE-ASSOCIATED LEUCINE-RICH REPEAT KINASE 2 REV DIMERIC GTPASE PROC.NATL.ACAD.SCI.USA V. 105 1499 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 133 families.
1 3D6T - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 2ZEJ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 101 families.
1 3D6T - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 2ZEJ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 70 families.
1 3D6T - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 2ZEJ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GDP; Similar ligands found: 160
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 GNP 0.839506 0.973684
6 9GM 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 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GPG 0.741573 0.961039
21 GDP BEF 0.741176 0.935065
22 GTP MG 0.732558 0.96
23 G3D 0.732558 0.986486
24 ALF 5GP 0.729412 0.888889
25 Y9Z 0.728261 0.902439
26 G5P 0.723404 0.973684
27 GFB 0.72043 0.961039
28 GTG 0.72043 0.936709
29 GDR 0.72043 0.961039
30 G4P 0.715909 0.986486
31 6CK 0.712766 0.936709
32 G3A 0.712766 0.973684
33 GDP ALF 0.7 0.888889
34 GDP AF3 0.7 0.888889
35 YGP 0.698925 0.901235
36 GKD 0.697917 0.961039
37 JB2 0.697917 0.961039
38 GDX 0.690722 0.973684
39 GPD 0.690722 0.925
40 GMP 0.684211 0.88
41 0O2 0.666667 0.986486
42 JB3 0.656863 0.948718
43 NGD 0.650485 0.961039
44 GDP 7MG 0.636364 0.911392
45 DGI 0.636364 0.923077
46 U2G 0.634615 0.936709
47 GPX 0.634409 0.946667
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 KB7 0.629214 0.82716
52 CG2 0.622642 0.936709
53 FEG 0.619048 0.879518
54 MGD 0.614679 0.891566
55 ZGP 0.613208 0.869048
56 GH3 0.612903 0.973333
57 3GP 0.611765 0.946667
58 MD1 0.607143 0.891566
59 PGD 0.59292 0.925
60 DGT 0.591398 0.923077
61 BGO 0.588785 0.924051
62 TPG 0.582609 0.840909
63 DBG 0.582609 0.948718
64 KBD 0.581633 0.82716
65 QBQ 0.576087 0.986486
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 KBJ 0.558824 0.797619
69 MGP 0.553191 0.961039
70 G4M 0.548387 0.880952
71 6G0 0.547368 0.961039
72 I2C FE2 CMO CMO 0.543103 0.808989
73 G1R G1R 0.542373 0.924051
74 P2G 0.527473 0.883117
75 PGD O 0.525 0.850575
76 ADP 0.522222 0.92
77 R5I 0.520833 0.946667
78 R7I 0.520833 0.946667
79 GGM 0.517544 0.901235
80 DG 0.516484 0.910256
81 DGP 0.516484 0.910256
82 P1G 0.516129 0.871795
83 CZF 0.515789 0.933333
84 G1G 0.508475 0.925
85 IMP 0.505495 0.959459
86 AKW 0.504425 0.890244
87 G C 0.504348 0.9
88 GPC 0.491525 0.879518
89 G7M 0.483871 0.948052
90 6AD 0.479592 0.841463
91 ATP 0.473684 0.92
92 HEJ 0.473684 0.92
93 G2Q 0.471154 0.961039
94 AQP 0.46875 0.92
95 5FA 0.46875 0.92
96 GTA 0.468468 0.936709
97 7DD 0.468085 0.906667
98 SGP 0.463158 0.82716
99 01G 0.462963 0.902439
100 HFD 0.459184 0.873418
101 JSQ 0.459184 0.873418
102 B4P 0.457447 0.894737
103 AP5 0.457447 0.894737
104 A2D 0.456522 0.894737
105 6YZ 0.455446 0.896104
106 ACQ 0.454545 0.896104
107 ANP 0.454545 0.896104
108 5GP 5GP 0.454545 0.883117
109 AT4 0.452632 0.884615
110 APC G U 0.451613 0.886076
111 PRT 0.449541 0.959459
112 ITT 0.447917 0.868421
113 BA3 0.446809 0.894737
114 C2E 0.444444 0.921053
115 35G 0.444444 0.933333
116 PCG 0.444444 0.933333
117 MGO 0.441176 0.864198
118 AN2 0.4375 0.907895
119 NO7 0.436893 0.860759
120 M33 0.43299 0.883117
121 UCG 0.429688 0.911392
122 ACP 0.428571 0.896104
123 MGQ 0.424528 0.935897
124 APR 0.424242 0.894737
125 7DT 0.424242 0.906667
126 AR6 0.424242 0.894737
127 M7G A2M G 0.422819 0.808989
128 93A 0.42268 0.833333
129 A4P 0.420168 0.869048
130 G8D 0.42 0.875
131 AD9 0.42 0.896104
132 AGS 0.42 0.873418
133 CA0 0.418367 0.896104
134 ATF 0.417476 0.884615
135 NYZ 0.415842 0.935897
136 GZ0 0.415254 0.948718
137 AGO 0.414634 0.888889
138 KG4 0.414141 0.896104
139 NIA 0.413043 0.82716
140 MGV 0.412844 0.890244
141 TAT 0.411765 0.884615
142 T99 0.411765 0.884615
143 ADQ 0.411215 0.871795
144 A1R 0.411215 0.839506
145 RGT 0.410714 0.909091
146 CGP 0.409836 0.86747
147 HQG 0.409524 0.907895
148 C1Z 0.409091 0.986486
149 AMP 0.408602 0.893333
150 A 0.408602 0.893333
151 UP5 0.40678 0.873418
152 C2R 0.406593 0.906667
153 AMZ 0.406593 0.918919
154 JBT 0.405882 0.778947
155 A22 0.40566 0.907895
156 25L 0.405405 0.907895
157 ADX 0.40404 0.809524
158 8OD 0.401961 0.946667
159 50T 0.4 0.883117
160 4TC 0.4 0.851852
Similar Ligands (3D)
Ligand no: 1; Ligand: GDP; Similar ligands found: 93
No: Ligand Similarity coefficient
1 ADP MG 0.9864
2 GDP MG 0.9797
3 DAT 0.9680
4 ALF GDP 0.9549
5 A12 0.9524
6 BEF GDP 0.9486
7 AU1 0.9476
8 CUU 0.9442
9 SON 0.9417
10 TYD 0.9414
11 M7G 0.9411
12 ADP ALF 0.9391
13 ADP BEF 0.9391
14 ADP AF3 0.9391
15 BEF ADP 0.9383
16 GAP 0.9328
17 O02 0.9303
18 G5A 0.9285
19 AP2 0.9265
20 5AL 0.9252
21 8GD 0.9250
22 M7M 0.9212
23 AV2 0.9211
24 DAL AMP 0.9209
25 PRX 0.9194
26 UDP 0.9193
27 8LE 0.9188
28 SRP 0.9155
29 SAM 0.9145
30 A5A 0.9126
31 GJV 0.9116
32 NWZ 0.9106
33 CDP 0.9093
34 MGT 0.9090
35 YYY 0.9086
36 5CA 0.9069
37 XMP 0.9066
38 EO7 0.9060
39 SSA 0.9052
40 DSH 0.9051
41 71V 0.9041
42 2A5 0.8973
43 TBD 0.8937
44 CDP MG 0.8931
45 SAH 0.8927
46 IMU 0.8919
47 6RE 0.8917
48 J7C 0.8916
49 7D3 0.8915
50 8LH 0.8914
51 DUD 0.8888
52 NX8 0.8885
53 6CG 0.8882
54 ABM 0.8881
55 8X1 0.8861
56 FMP 0.8855
57 LMS 0.8847
58 8GM 0.8842
59 DTP 0.8842
60 D4D 0.8817
61 C8M 0.8813
62 EEM 0.8812
63 SFG 0.8795
64 8OP 0.8780
65 ADP PO3 0.8775
66 D5M 0.8773
67 IRP 0.8767
68 PAP 0.8765
69 HDV 0.8759
70 ATR 0.8755
71 APC 0.8746
72 N5O 0.8734
73 A3N 0.8728
74 AS 0.8705
75 ATY 0.8684
76 54H 0.8676
77 TSB 0.8674
78 ME8 0.8672
79 HF7 0.8667
80 6MA 0.8654
81 SAI 0.8651
82 DUN 0.8649
83 LSS 0.8640
84 5FU 0.8638
85 P5A 0.8634
86 8QN 0.8633
87 DZ4 0.8609
88 CNU 0.8603
89 NVA LMS 0.8600
90 FNU 0.8593
91 TKW 0.8580
92 MOD 0.8567
93 MSP 0.8549
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2ZEJ; Ligand: GDP; Similar sites found with APoc: 62
This union binding pocket(no: 1) in the query (biounit: 2zej.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 3PQC GDP 1.63043
2 4J0Q GDP 4.8913
3 4J0Q GDP 4.8913
4 4J0Q GDP 4.8913
5 5W75 GDP 4.8913
6 5W75 GDP 4.8913
7 4P3Y GDP 5.07614
8 3U6B GDP 5.07614
9 3U6K GDP 5.07614
10 1D8T GDP 5.08906
11 5W7Q GDP 5.63003
12 5CK5 GDP 5.97826
13 5CK5 GDP 5.97826
14 5CK5 GDP 5.97826
15 1KK1 GNP 6.52174
16 2AWN ADP 6.52174
17 2AWN ADP 6.52174
18 2AWN ADP 6.52174
19 2AWN ADP 6.52174
20 2WJG GDP 6.52174
21 5GOE GDP 6.52174
22 1SKQ GDP 7.06522
23 1SKQ GDP 7.06522
24 5FG3 GDP 7.6087
25 2WIC GNP 7.6087
26 6G14 G4P 8.15217
27 5YT0 GDP 8.15217
28 4R98 GNH 9.23913
29 1YRB GDP 10.3261
30 1YRB GDP 10.3261
31 5W76 GDP 11.413
32 3CNL GNP 11.9565
33 3EC1 GDP 13.587
34 1FZQ GDP 17.9348
35 2QN6 GDP 18.2796
36 6A8D GDP 19.5652
37 1RE0 GDP 21.3415
38 3WY9 GDP 21.875
39 1ZJ6 G3D 22.2826
40 3N5C GDP 24.0741
41 3Q72 GNP 28.3133
42 2HT6 GDP 31.0345
43 4DKX GDP 33.6957
44 1S8F GDP 34.4633
45 1S8F GDP 34.4633
46 1VG1 GDP 35.3261
47 1VG9 GDP 35.3261
48 1Z0A GDP 36.7816
49 1Z0A GDP 36.7816
50 5O74 GDP 38.8889
51 5O74 GDP 38.8889
52 5O74 GDP 38.8889
53 5BXQ GDP 42.3913
54 5BXQ GDP 42.3913
55 3GJ0 GDP 42.3913
56 3GJ3 GDP 42.3913
57 5BXQ GDP 42.3913
58 3CH5 GDP 42.3913
59 3GJ5 GDP 44.0217
60 3GJ4 GDP 44.0217
61 3GJ7 GDP 44.0217
62 3GJ5 GDP 44.0217
Pocket No.: 2; Query (leader) PDB : 2ZEJ; Ligand: GDP; Similar sites found with APoc: 65
This union binding pocket(no: 2) in the query (biounit: 2zej.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 4LC1 GDP 3.80435
2 4LC1 GDP 3.80435
3 4J0Q GDP 4.8913
4 4J0Q GDP 4.8913
5 4J0Q GDP 4.8913
6 5W75 GDP 4.8913
7 5W75 GDP 4.8913
8 4P3Y GDP 5.07614
9 3U6B GDP 5.07614
10 3U6K GDP 5.07614
11 1D8T GDP 5.08906
12 5W7Q GDP 5.63003
13 5CK5 GDP 5.97826
14 5CK5 GDP 5.97826
15 5CK5 GDP 5.97826
16 1KK1 GNP 6.52174
17 2AWN ADP 6.52174
18 2WJG GDP 6.52174
19 2AWN ADP 6.52174
20 2AWN ADP 6.52174
21 2AWN ADP 6.52174
22 5GOE GDP 6.52174
23 1SKQ GDP 7.06522
24 1SKQ GDP 7.06522
25 5FG3 GDP 7.6087
26 2WIC GNP 7.6087
27 6G14 G4P 8.15217
28 5YT0 GDP 8.15217
29 4R98 GNH 9.23913
30 1YRB GDP 10.3261
31 1YRB GDP 10.3261
32 5W76 GDP 11.413
33 3CNL GNP 11.9565
34 3EC1 GDP 13.587
35 1FZQ GDP 17.9348
36 2QN6 GDP 18.2796
37 6A8D GDP 19.5652
38 1RE0 GDP 21.3415
39 3WY9 GDP 21.875
40 1ZJ6 G3D 22.2826
41 3N5C GDP 24.0741
42 3Q72 GNP 28.3133
43 2HT6 GDP 31.0345
44 4DKX GDP 33.6957
45 1S8F GDP 34.4633
46 1S8F GDP 34.4633
47 1VG1 GDP 35.3261
48 1VG9 GDP 35.3261
49 1Z0A GDP 36.7816
50 1Z0A GDP 36.7816
51 1Z0A GDP 36.7816
52 1Z0A GDP 36.7816
53 5O74 GDP 38.8889
54 5O74 GDP 38.8889
55 5O74 GDP 38.8889
56 5BXQ GDP 42.3913
57 5BXQ GDP 42.3913
58 3GJ0 GDP 42.3913
59 3GJ3 GDP 42.3913
60 5BXQ GDP 42.3913
61 3CH5 GDP 42.3913
62 3GJ5 GDP 44.0217
63 3GJ7 GDP 44.0217
64 3GJ4 GDP 44.0217
65 3GJ5 GDP 44.0217
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