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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;
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443.201 C10 H15 N5 O11 P2 c1nc2...
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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: 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 : 3CB2; Ligand: GDP; Similar sites found with APoc: 161
This union binding pocket(no: 1) in the query (biounit: 3cb2.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1F6D UDP 0.797872
2 3CTY FAD 1.25392
3 3NTD FAD 1.26316
4 3PIJ FRU 1.26316
5 1QO8 FAD 1.47368
6 5Y79 3PG 1.51976
7 4EDF UPG 1.68421
8 1D4D FAD 1.68421
9 4YNU LGC 1.68421
10 4YNU FAD 1.68421
11 3BP1 GUN 1.72414
12 5LJW ANP 1.72911
13 3ITJ CIT 1.77515
14 5DK4 5BX 1.82371
15 5DK4 ATP 1.82371
16 1XHC FAD 1.89474
17 1SB8 NAD 1.98864
18 1SB8 UD2 1.98864
19 3CV2 COA 2.10526
20 4D86 ADP 2.16867
21 4EMI NAD 2.19512
22 1I2B UPG 2.22772
23 1I2B USQ 2.22772
24 1I2B NAD 2.22772
25 4UP3 FAD 2.2293
26 5VN0 NAI 2.31579
27 4M52 M52 2.36052
28 4M52 FAD 2.36052
29 2A8X FAD 2.37069
30 4A59 AMP 2.52632
31 3DMH GMP 2.52632
32 3RFV NAI 2.62172
33 1PJS NAD 2.62582
34 4RFM 3P6 2.63158
35 1BZL FAD 2.73684
36 3CGD FAD 2.73684
37 3CGD COA 2.73684
38 3CGD NAD 2.73684
39 4JDR FAD 2.74262
40 3LU1 NAD 2.74725
41 3V1S 0LH 2.79503
42 5JCM NAD 2.88248
43 5JCM FAD 2.88248
44 5JCM ISD 2.88248
45 1NVM NAD 2.88462
46 2WPF FAD 2.94737
47 2WPF WPF 2.94737
48 1FEC FAD 2.94737
49 1GTE FAD 2.94737
50 2RI1 GLP 2.97872
51 2PZM NAD 3.0303
52 2PZM UDP 3.0303
53 1BXK NAD 3.09859
54 5J60 FAD 3.125
55 4J36 1HR 3.13253
56 4J36 FAD 3.13253
57 1DJN ADP 3.15789
58 5THQ NDP 3.30882
59 6GAS FAD 3.32326
60 3LAD FAD 3.36842
61 2OZ5 7XY 3.37838
62 2DPY ADP 3.42466
63 1TDF FAD 3.48101
64 1MO9 FAD 3.57895
65 1MO9 KPC 3.57895
66 5U8U FAD 3.57895
67 5CKS GAL 3.7037
68 6GAR FAD 3.72493
69 5TWB FAD 3.77907
70 3EWA ANP 3.78947
71 6DW2 HD4 3.79747
72 4UAP NGA 3.94737
73 1Y9G FRU 4
74 5A96 GTP 4.01606
75 4ZGM 32M 4.09836
76 6BYF CIT 4.11765
77 5Y80 IRE 4.15335
78 1O94 ADP 4.16667
79 4NTC FAD 4.1791
80 1FFU CDP 4.18118
81 1HKU NAD 4.21053
82 5BRT FAD 4.21053
83 1V59 FAD 4.39331
84 2Y4O DLL 4.51467
85 1R6D DAU 4.74777
86 1R6D NAD 4.74777
87 4HXY NDP 4.79452
88 4BV6 FAD 4.84211
89 2FZW NAD 4.84211
90 5BVA FAD 4.88998
91 2GDJ ANP 4.92424
92 5YRI GLC GLC 4.92958
93 5YRG BGC GLC 4.92958
94 5YRJ BGC GLC 4.92958
95 4C3Y FAD 5.05263
96 4C3Y ANB 5.05263
97 4PIV NDP 5.05263
98 4ZRN NAD 5.12821
99 4ZRN UPG 5.12821
100 1Q8Q MAN MMA 5.15873
101 6FP4 E1T 5.18395
102 1GET NAP 5.33333
103 1GET FAD 5.33333
104 2FR1 NDP 5.34979
105 5C1M OLC 5.6
106 1EZ4 NAD 5.66038
107 2FMD MAN MAN 5.83333
108 5J5Z FAD 5.89474
109 5DF1 58X 5.97826
110 5DF1 NAP 5.97826
111 6B2W AG2 6.00601
112 4ZVV GN0 6.0241
113 4ZVV NAD 6.0241
114 4WZ8 3W7 6.10526
115 2PZE ATP 6.11354
116 4J56 FAD 6.14035
117 2RAB NAD 6.2635
118 2RAB FAD 6.2635
119 4DXD GDP 6.31313
120 2ZXI FAD 6.31579
121 2RHO GDP 6.46154
122 2RHO GSP 6.46154
123 2P3V SRT 6.64062
124 4NTO 1PW 6.76329
125 1UDB NAD 6.80473
126 1UDB UFG 6.80473
127 5MIT FAD 7.03364
128 5MIT NAP 7.03364
129 3VY6 BGC BGC 7.0922
130 2BSA NAP 7.26073
131 5K0A FAD 7.27273
132 3GD4 NAD 7.57895
133 4D4U FUC NDG GAL FUC 7.61905
134 5XDT GDP 7.79221
135 5XDT MB3 7.79221
136 5W7B MYR 7.80142
137 3ZBQ GDP 8.10811
138 2VZZ SCA 8.25688
139 1W5F G2P 8.49858
140 2F5Z FAD 9.375
141 4W6Z 8ID 9.79827
142 3W54 RNB 10.3343
143 2Q1W NAD 10.8108
144 5NUE NAD 10.8434
145 5NUF NAD 10.8434
146 3M89 GSP 11.2412
147 2GUD MAN 13.1148
148 2BQP GLC 13.2479
149 5ODQ FAD 13.5714
150 2VAP GDP 13.7363
151 1OFS SUC 14.9733
152 1OFU GDP 15.9375
153 1RQ2 CIT 15.9686
154 2R75 01G 15.9763
155 1LES GLC FRU 16.0221
156 5C9J DAO 17.1717
157 1PS9 FAD 17.6842
158 4EI7 GDP 17.9949
159 4RJD TFP 25.7576
160 3RNM FAD 29.3103
161 2BTO GTP 49.6829
Pocket No.: 2; Query (leader) PDB : 3CB2; Ligand: GDP; Similar sites found with APoc: 94
This union binding pocket(no: 2) in the query (biounit: 3cb2.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 3KO0 TFP None
2 3QJ4 FAD 1.46199
3 2WOX NDP 1.68421
4 2WME NAP 1.68421
5 3ITJ FAD 1.77515
6 4JNE ATP 1.89474
7 1YB5 NAP 1.9943
8 4REP FAD 2.10526
9 3AB1 FAD 2.22222
10 1FL2 FAD 2.25806
11 4ZNO SUC 2.31579
12 4K7O EKZ 2.38095
13 4Q6R SIN 2.52632
14 2GVV DI9 2.54777
15 4D7E FAD 2.5641
16 1ZK7 FAD 2.56959
17 4YKG NAD 2.73684
18 4YKG FAD 2.73684
19 4IV9 FAD 2.73684
20 5B4B LP5 2.82258
21 3OF1 CMP 2.84553
22 3O9Z NAD 2.88462
23 2VVL FAD 2.94737
24 5TS5 FAD 2.94737
25 2IID PHE 2.94737
26 2IID FAD 2.94737
27 3ROE THM 2.94737
28 1ZGS XMM 3.13199
29 5OPM DTP 3.15789
30 1GV0 NAD 3.22581
31 3PNA CMP 3.24675
32 4ZUL UN1 3.36842
33 1IXI 2HP 3.42679
34 4HA6 FAD 3.54331
35 3QVP FAD 3.57895
36 4OUE IPT 3.62473
37 1XXR MAN 3.72671
38 4MG9 27K 3.92157
39 5HCY 60D 3.92749
40 4TV1 36M 3.98406
41 5TTJ FAD 4.21053
42 4KVL PLM 4.42105
43 3GDN HBX 4.42105
44 3GDN FAD 4.42105
45 3O01 DXC 4.54545
46 2DTX BMA 4.54545
47 1LVL FAD 4.58515
48 1LOJ URI 4.5977
49 1LOJ U 4.5977
50 2OBM ADP 4.61095
51 5YRL GLC GLC 4.92958
52 5YRF GLC GLC 4.92958
53 5YRM BGC GLC 4.92958
54 3F8D FAD 4.95356
55 4M00 SUC 5.05263
56 2GMM MAN MAN 5.15873
57 1Q8S MAN MMA 5.15873
58 2GNM MAN 5.15873
59 1UKG MMA 5.15873
60 2GN3 MMA 5.15873
61 2PHT MAN MAN MAN 5.15873
62 2PHX MAN MAN 5.15873
63 2GND MAN 5.15873
64 2PHU MAN MAN 5.15873
65 1Q8O MAN MMA 5.15873
66 1Q8V MAN MAN 5.15873
67 3L4S 3PG 5.35714
68 3L4S NAD 5.35714
69 3G4Q MCH 5.47945
70 5YB7 FAD 5.68421
71 5YB7 ORN 5.68421
72 3B5J 12D 5.76132
73 5EXW 7DT 6
74 5LX9 OLB 6.18893
75 1GQ2 NAP 6.52632
76 1H82 FAD 6.5678
77 2YG3 FAD 6.62252
78 1YQZ FAD 6.84932
79 5J6Y BGC 7.44681
80 5J6Y GLC 7.44681
81 4WZA ADP 7.6087
82 4WZA ACP 7.6087
83 1RV1 IMZ 8.23529
84 5JWC FAD 8.25336
85 1VBO MAN 10.0671
86 2C3W GLC GLC GLC GLC 10.7843
87 1E6E FAD 10.9375
88 4GUT FAD 12.0968
89 4YSX FAD 12.766
90 2GUC MAN 13.1148
91 2HYQ MAN MAN 13.1148
92 2HYR BGC GLC 13.1148
93 5TQZ GLC 26
94 4WG0 CHD 40
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