Receptor
PDB id Resolution Class Description Source Keywords
2X77 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LEISHMANIA MAJOR ADP RIBOSYLATION FACTOR-LIKE 1. LEISHMANIA MAJOR GTP-BINDING PROTEIN SMALL GTPASE NUCLEOTIDE-BINDING
Ref.: CRYSTAL STRUCTURE OF LEISHMANIA MAJOR ADP RIBOSYLATION FACTOR-LIKE 1 AND A CLASSIFICATION OF RELATED GTPASE FAMILY MEMBERS IN THIS KINETOPLASTID. MOL.BIOCHEM.PARASITOL. V. 174 141 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:188;
B:188;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:189;
B:189;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2X77 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LEISHMANIA MAJOR ADP RIBOSYLATION FACTOR-LIKE 1. LEISHMANIA MAJOR GTP-BINDING PROTEIN SMALL GTPASE NUCLEOTIDE-BINDING
Ref.: CRYSTAL STRUCTURE OF LEISHMANIA MAJOR ADP RIBOSYLATION FACTOR-LIKE 1 AND A CLASSIFICATION OF RELATED GTPASE FAMILY MEMBERS IN THIS KINETOPLASTID. MOL.BIOCHEM.PARASITOL. V. 174 141 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 2X77 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 2X77 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 1RRG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1HUR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1O3Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
5 1YZG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 3AQ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
10 4YLG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 1MR3 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 4V0K - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4V0L - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 2X77 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1RRG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 1HUR - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 1O3Y - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 1FZQ Kd = 24 nM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 1Z6Y - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 1ZJ6 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
10 1YZG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
11 3N5C - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
12 1E0S - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
13 1ZD9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 2AL7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 3AQ4 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 4Y0V - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 4YLG - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
18 1MR3 - G3D C10 H16 N5 O14 P3 c1nc2c(n1[....
19 4BAS - GNP C10 H17 N6 O13 P3 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 : 2X77; Ligand: GDP; Similar sites found with APoc: 96
This union binding pocket(no: 1) in the query (biounit: 2x77.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1CLU DBG None
2 1SKQ GDP 1.5873
3 6BVJ GNP 2.1164
4 6BVK GNP 2.1164
5 6BVI GNP 2.1164
6 6D5H GNP 2.1164
7 6BVL GNP 2.1164
8 6D5E GNP 2.1164
9 6D5G GNP 2.1164
10 6D5J GNP 2.1164
11 2RCN GDP 2.6455
12 2QN6 GDP 3.7037
13 1D8T GDP 4.2328
14 2HCJ GDP 4.2328
15 2C5L GTP 4.2735
16 1SVI GDP 4.7619
17 2C78 GNP 4.7619
18 1WQ1 GDP 6.34921
19 4LC1 GDP 6.34921
20 1KK1 GNP 6.34921
21 3Q72 GNP 6.62651
22 1G7S GDP 7.40741
23 1TQ4 GDP 8.99471
24 1MKY GDP 9.52381
25 5YT0 GDP 10.0529
26 5FG3 GDP 10.0529
27 4HDO GNP 10.0529
28 1GUA GNP 10.0529
29 1YRB GDP 12.6984
30 1I4D GDP 13.2275
31 2J0V GDP 13.2275
32 1WF3 GNP 13.2275
33 4B47 GDP 13.7566
34 1DS6 GDP 13.7566
35 1RYH GNP 13.7566
36 2FJU GSP 13.7566
37 1MH1 GNP 14.2857
38 2WKQ GTP 14.8148
39 1E96 GTP 14.8148
40 3Q85 GNP 15.3846
41 5TB5 GDP 17.2973
42 5TAR GDP 17.2973
43 3WXM GTP 17.4603
44 3EC1 GDP 17.9894
45 4D0N GDP 18.5185
46 5UWP GNP 19.5767
47 4HAT GNP 19.5767
48 5DIF GNP 19.5767
49 6CIT GNP 19.5767
50 5UWW GNP 19.5767
51 5UWU GNP 19.5767
52 5UWO GNP 19.5767
53 5DHF GNP 19.5767
54 5UWS GNP 19.5767
55 3GJ3 GDP 19.5767
56 5UWT GNP 19.5767
57 5UWH GNP 19.5767
58 3GJ0 GDP 19.5767
59 3GJ4 GDP 19.5767
60 3M1I GTP 19.5767
61 3GJ7 GDP 19.5767
62 3GJ8 GDP 19.5767
63 3GJ5 GDP 19.5767
64 5BXQ GDP 19.5767
65 3CH5 GDP 19.5767
66 1WA5 GTP 19.8864
67 5CK5 GDP 20.1058
68 2CJW GDP 20.1058
69 1VG0 GDP 20.1058
70 1VG1 GDP 20.5405
71 1VG9 GDP 20.5405
72 1Z2A GDP 21.164
73 2HT6 GDP 21.2644
74 5HCN GCP 21.6931
75 3RWO GDP 23.2804
76 3T5G GDP 27.6243
77 2A9K GDP 30.1587
78 4DCT GDP 30.6878
79 1ZC3 GNP 31.4286
80 1S8F GDP 31.6384
81 5O74 GDP 31.746
82 1Z0J GTP 32.3529
83 1YVD GNP 33.1361
84 5M04 GDP 33.3333
85 1U8Z GDP 33.3333
86 1OIX GDP 33.8624
87 1Z0A GDP 33.8624
88 1OIV GDP 34.3915
89 3BC1 GNP 35.4497
90 1Z0F GDP 35.9788
91 3RAB GNP 36.0947
92 2A5J GDP 38.6243
93 2FFQ GSP 39.1813
94 5UWQ GNP 40.9091
95 1F6B GDP 41.7989
96 1G16 GDP 44.1176
Pocket No.: 2; Query (leader) PDB : 2X77; 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: 2x77.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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