Receptor
PDB id Resolution Class Description Source Keywords
3CB2 2.3 Å EC: 3.6.5.6 CRYSTAL STRUCTURE OF HUMAN GAMMA-TUBULIN BOUND TO GDP HOMO SAPIENS TUBULIN LATTICE MICROTUBULE NUCLEATION GTPASE LATERAL INTERACTION STRUCTURAL PROTEIN HYDROLASE
Ref.: THE LATTICE AS ALLOSTERIC EFFECTOR: STRUCTURAL STUDIES OF ALPHABETA- AND GAMMA-TUBULIN CLARIFY THE ROLE OF GTP IN MICROTUBULE ASSEMBLY PROC.NATL.ACAD.SCI.USA V. 105 5378 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:500;
B:501;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3CB2 2.3 Å EC: 3.6.5.6 CRYSTAL STRUCTURE OF HUMAN GAMMA-TUBULIN BOUND TO GDP HOMO SAPIENS TUBULIN LATTICE MICROTUBULE NUCLEATION GTPASE LATERAL INTERACTION STRUCTURAL PROTEIN HYDROLASE
Ref.: THE LATTICE AS ALLOSTERIC EFFECTOR: STRUCTURAL STUDIES OF ALPHABETA- AND GAMMA-TUBULIN CLARIFY THE ROLE OF GTP IN MICROTUBULE ASSEMBLY PROC.NATL.ACAD.SCI.USA V. 105 5378 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3CB2 - 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 1 families.
1 3CB2 - 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 1 families.
1 3CB2 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 153
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 G 0.828947 0.986486
7 5GP 0.828947 0.986486
8 G1R 0.82716 0.986667
9 GCP 0.82716 0.973684
10 GSP 0.817073 0.948718
11 GAV 0.797619 0.961039
12 GMV 0.792683 0.973684
13 G2P 0.77381 0.961039
14 G2R 0.770115 0.961039
15 GDP MG 0.759036 0.923077
16 GP2 0.756098 0.961039
17 GDP BEF 0.75 0.9
18 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GDC 0.747253 0.961039
21 GPG 0.741573 0.961039
22 G3D 0.732558 0.986486
23 ALF 5GP 0.729412 0.888889
24 Y9Z 0.728261 0.902439
25 GTP MG 0.724138 0.923077
26 BEF GDP 0.724138 0.888889
27 G5P 0.723404 0.973684
28 GFB 0.72043 0.961039
29 GTG 0.72043 0.936709
30 GDR 0.72043 0.961039
31 G4P 0.715909 0.986486
32 GCP G 0.715909 0.935065
33 6CK 0.712766 0.936709
34 G3A 0.712766 0.973684
35 GDP ALF 0.7 0.888889
36 GDP AF3 0.7 0.888889
37 YGP 0.698925 0.901235
38 JB2 0.697917 0.961039
39 GKD 0.697917 0.961039
40 GDX 0.690722 0.973684
41 GPD 0.690722 0.925
42 GMP 0.684211 0.88
43 0O2 0.666667 0.986486
44 G G 0.659574 0.935065
45 JB3 0.656863 0.948718
46 NGD 0.650485 0.961039
47 GDP 7MG 0.636364 0.911392
48 DGI 0.636364 0.923077
49 U2G 0.634615 0.936709
50 GPX 0.634409 0.946667
51 IDP 0.632184 0.972973
52 2MD 0.632075 0.891566
53 CAG 0.62963 0.880952
54 CG2 0.622642 0.936709
55 FEG 0.619048 0.879518
56 MGD 0.614679 0.891566
57 ZGP 0.613208 0.869048
58 GH3 0.612903 0.973333
59 3GP 0.611765 0.946667
60 MD1 0.607143 0.891566
61 PGD 0.59292 0.925
62 DGT 0.591398 0.923077
63 BGO 0.588785 0.924051
64 TPG 0.582609 0.840909
65 DBG 0.582609 0.948718
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 I2C FE2 CMO CMO 0.566372 0.808989
69 G A A A 0.553571 0.923077
70 MGP 0.553191 0.961039
71 U A G G 0.548673 0.935065
72 G4M 0.548387 0.880952
73 6G0 0.547368 0.961039
74 G1R G1R 0.542373 0.924051
75 P2G 0.527473 0.883117
76 PGD O 0.525 0.850575
77 ADP 0.522222 0.92
78 GGM 0.517544 0.901235
79 DG 0.516484 0.910256
80 DGP 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G G U 0.509259 0.935065
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 G C 0.504348 0.9
86 GPC 0.491525 0.879518
87 G7M 0.483871 0.948052
88 6AD 0.479592 0.841463
89 ATP 0.473684 0.92
90 G2Q 0.471154 0.961039
91 U G A 0.469697 0.888889
92 5FA 0.46875 0.92
93 AQP 0.46875 0.92
94 GTA 0.468468 0.936709
95 7DD 0.468085 0.906667
96 G G G RPC 0.466102 0.875
97 SGP 0.463158 0.82716
98 01G 0.462963 0.902439
99 B4P 0.457447 0.894737
100 AP5 0.457447 0.894737
101 A2D 0.456522 0.894737
102 G G G C 0.455285 0.9125
103 ACQ 0.454545 0.896104
104 5GP 5GP 0.454545 0.883117
105 ANP 0.454545 0.896104
106 A G C C 0.451613 0.911392
107 APC G U 0.45082 0.886076
108 G U34 0.449153 0.888889
109 DG DG 0.448598 0.865854
110 ITT 0.447917 0.868421
111 BA3 0.446809 0.894737
112 35G 0.444444 0.933333
113 C2E 0.444444 0.921053
114 PCG 0.444444 0.933333
115 MGO 0.441176 0.864198
116 AN2 0.4375 0.907895
117 G C C C 0.4375 0.924051
118 M33 0.43299 0.883117
119 UCG 0.429688 0.911392
120 A G U 0.42963 0.888889
121 ACP 0.428571 0.896104
122 MGQ 0.424528 0.935897
123 7DT 0.424242 0.906667
124 APR 0.424242 0.894737
125 AR6 0.424242 0.894737
126 93A 0.42268 0.833333
127 A4P 0.420168 0.869048
128 SAP 0.42 0.873418
129 AD9 0.42 0.896104
130 AGS 0.42 0.873418
131 G8D 0.42 0.875
132 CA0 0.418367 0.896104
133 ATF 0.417476 0.884615
134 AGO 0.414634 0.888889
135 NIA 0.413043 0.82716
136 MGV 0.412844 0.890244
137 TAT 0.411765 0.884615
138 A1R 0.411215 0.839506
139 ADQ 0.411215 0.871795
140 RGT 0.410714 0.909091
141 CGP 0.409836 0.86747
142 AMP 0.408602 0.893333
143 A 0.408602 0.893333
144 UP5 0.40678 0.873418
145 C2R 0.406593 0.906667
146 AMZ 0.406593 0.918919
147 JBT 0.405882 0.778947
148 A22 0.40566 0.907895
149 25L 0.405405 0.907895
150 ADX 0.40404 0.809524
151 8OD 0.401961 0.946667
152 4TC 0.4 0.851852
153 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3CB2; Ligand: GDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3cb2.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3CB2; Ligand: GDP; Similar sites found: 61
This union binding pocket(no: 2) in the query (biounit: 3cb2.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KO0 TFP 0.006955 0.43283 None
2 3ITJ CIT 0.003901 0.42116 1.77515
3 4JNE ATP 0.01114 0.40302 1.89474
4 1SB8 UD2 0.04053 0.40216 1.98864
5 1SB8 NAD 0.0355 0.40216 1.98864
6 3CV2 COA 0.01489 0.41491 2.10526
7 4ZNO SUC 0.006449 0.42537 2.31579
8 4K7O EKZ 0.01832 0.40606 2.38095
9 4Q6R SIN 0.01192 0.41439 2.52632
10 3OF1 CMP 0.01104 0.40789 2.84553
11 2WPF WPF 0.0493 0.41598 2.94737
12 2WPF FAD 0.04845 0.41598 2.94737
13 1GV0 NAD 0.01776 0.40046 3.22581
14 3PNA CMP 0.01219 0.41007 3.24675
15 2DPY ADP 0.01735 0.40683 3.42466
16 1IXI 2HP 0.01243 0.4156 3.42679
17 1XXR MAN 0.01757 0.40452 3.72671
18 4TV1 36M 0.01706 0.4072 3.98406
19 4ZGM 32M 0.02542 0.40643 4.09836
20 4YDS ATP 0.01683 0.4075 4.38596
21 3GDN HBX 0.03909 0.40295 4.42105
22 3GDN FAD 0.02859 0.40278 4.42105
23 1LOJ U 0.01882 0.40675 4.5977
24 2OBM ADP 0.01799 0.40996 4.61095
25 1R6D NAD 0.04047 0.40287 4.74777
26 1R6D DAU 0.04115 0.40183 4.74777
27 2GDJ ANP 0.003604 0.43125 4.92424
28 4M00 SUC 0.002834 0.43593 5.05263
29 2GMM MAN MAN 0.005695 0.42984 5.15873
30 1Q8Q MAN MMA 0.009842 0.42078 5.15873
31 1Q8S MAN MMA 0.01311 0.41343 5.15873
32 2GNM MAN 0.01113 0.41327 5.15873
33 1UKG MMA 0.01088 0.41283 5.15873
34 2GN3 MMA 0.004793 0.40813 5.15873
35 2PHT MAN MAN MAN 0.01799 0.40723 5.15873
36 2GND MAN 0.01807 0.40496 5.15873
37 2PHU MAN MAN 0.01878 0.4038 5.15873
38 3B5J 12D 0.01921 0.40458 5.76132
39 4DXD GDP 0.00000007125 0.53551 6.31313
40 2RHO GSP 0.000002423 0.56827 6.46154
41 2RHO GDP 0.000004937 0.52079 6.46154
42 5J6Y GLC 0.02486 0.40625 7.44681
43 5J6Y BGC 0.02486 0.40625 7.44681
44 5XDT GDP 0.00000003768 0.65501 7.79221
45 5XDT MB3 0.00000007403 0.65501 7.79221
46 3ZBQ GDP 0.0000001319 0.58089 8.10811
47 1W5F G2P 0.000002477 0.48104 8.49858
48 4W6Z 8ID 0.02031 0.40438 9.79827
49 1VBO MAN 0.004978 0.43604 10.0671
50 1E6E FAD 0.02146 0.40323 10.9375
51 3M89 GSP 0.0000002389 0.62189 11.2412
52 2BQP GLC 0.007058 0.42839 13.2479
53 2VAP GDP 0.0000001474 0.49784 13.7363
54 1OFS SUC 0.01438 0.41132 14.9733
55 1OFU GDP 0.0000001079 0.58215 15.9375
56 1RQ2 CIT 0.0000001971 0.54836 15.9686
57 2R75 01G 0.00000007642 0.51878 15.9763
58 1LES GLC FRU 0.005475 0.42792 16.0221
59 4EI7 GDP 0.00000000252 0.61101 17.9949
60 5TQZ GLC 0.01197 0.41216 26
61 2BTO GTP 0.00000000007926 0.64819 49.6829
Feedback