Receptor
PDB id Resolution Class Description Source Keywords
4LC1 1.8 Å EC: 3.-.-.- MEAB, A BACTERIAL HOMOLOG OF MMAA, BOUND TO GDP AND CRYSTALL THE PRESENCE OF GDP AND [ALF4]- METHYLOBACTERIUM EXTORQUENS ALPHA AND BETA PROTEIN METALLOCHAPERONE CHAPERONE
Ref.: AUTOINHIBITION AND SIGNALING BY THE SWITCH II MOTIF G-PROTEIN CHAPERONE OF A RADICAL B12 ENZYME. J.BIOL.CHEM. V. 288 30980 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP B:401;
A:401;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
GOL A:402;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4LC1 1.8 Å EC: 3.-.-.- MEAB, A BACTERIAL HOMOLOG OF MMAA, BOUND TO GDP AND CRYSTALL THE PRESENCE OF GDP AND [ALF4]- METHYLOBACTERIUM EXTORQUENS ALPHA AND BETA PROTEIN METALLOCHAPERONE CHAPERONE
Ref.: AUTOINHIBITION AND SIGNALING BY THE SWITCH II MOTIF G-PROTEIN CHAPERONE OF A RADICAL B12 ENZYME. J.BIOL.CHEM. V. 288 30980 2013
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 4JYB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 2QM7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 4JYC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 4LC1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 4JYB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 2QM7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 4JYC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 4LC1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 173 families.
1 3MD0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4JYB - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
3 2QM7 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 4JYC - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 4LC1 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3TK1 - 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 : 4LC1; Ligand: GDP; Similar sites found with APoc: 123
This union binding pocket(no: 1) in the query (biounit: 4lc1.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5WDR GNP 1.16959
2 2A5J GDP 1.57068
3 5FG3 GDP 1.78042
4 5YT0 GDP 1.78042
5 5GOE GDP 1.78042
6 3MJH GTP 1.78571
7 5CK5 GDP 2.21519
8 3SFV GDP 2.67062
9 5W76 GDP 2.96736
10 5O74 GDP 3.04569
11 4DKX GDP 3.24074
12 1X1R GDP 3.37079
13 2RCN GDP 3.56083
14 5LEF GTP 3.66492
15 4B47 GDP 3.85757
16 3WY9 GDP 3.91705
17 3WYA GDP 3.91705
18 4YLG GDP 4.04624
19 2FFQ GSP 4.09357
20 1D2E GDP 4.1543
21 2C78 GNP 4.1543
22 5W7Q GDP 4.1543
23 2C77 GNP 4.1543
24 1SKQ GDP 4.1543
25 3RWO GDP 4.32432
26 4ZKD GDP 4.45104
27 3GJ3 GDP 4.52489
28 3GJ4 GDP 4.52489
29 3GJ5 GDP 4.52489
30 1TQ4 GDP 4.74777
31 1CLU DBG 4.81928
32 1MKY GDP 5.04451
33 5SZH GNP 5.22876
34 1OIV GDP 5.2356
35 1OIX GDP 5.2356
36 3T5G GDP 5.26316
37 1Z06 GNP 5.29101
38 1Z0F GDP 5.58659
39 5JCZ GDP 5.58659
40 5M04 GDP 5.63798
41 1PUJ GNP 5.67376
42 3NKV GNP 5.71429
43 4V0K GDP 5.91716
44 1YRB GDP 6.10687
45 3N5C GDP 6.17284
46 4J0Q GDP 6.23145
47 2X77 GDP 6.34921
48 1VG9 GDP 6.48649
49 1VG1 GDP 6.48649
50 3AQ4 GDP 6.52174
51 1G7C 5GP 6.55022
52 3BC1 GNP 6.66667
53 1WA5 GTP 6.81818
54 1Z0J GTP 7.05882
55 1YVD GNP 7.10059
56 1GUA GNP 7.18563
57 5HCN GCP 7.27969
58 1G7S GDP 7.40741
59 3U6B GDP 7.4184
60 4G5G GDP 7.4184
61 5JBQ GDP 7.4184
62 1D8T GDP 7.4184
63 4P3Y GDP 7.4184
64 3U6K GDP 7.4184
65 2HCJ GDP 7.46269
66 1UPT GTP 7.60234
67 1FZQ GDP 7.73481
68 1MR3 G3D 7.73481
69 4HDO GNP 7.76398
70 4HDQ GNP 7.76398
71 1RE0 GDP 7.92683
72 4HAT GNP 8.01187
73 5UWQ GNP 8.01187
74 3M1I GTP 8.01187
75 5UWP GNP 8.01187
76 6CIT GNP 8.01187
77 5UWO GNP 8.01187
78 5DIF GNP 8.01187
79 5UWI GNP 8.01187
80 5UWU GNP 8.01187
81 5UWR GNP 8.01187
82 5UWW GNP 8.01187
83 5DHF GNP 8.01187
84 5UWS GNP 8.01187
85 5UWH GNP 8.01187
86 5UWT GNP 8.01187
87 1KK1 GNP 8.30861
88 2CJW GDP 8.33333
89 1YZG GDP 8.37989
90 2WJH GDP 8.43373
91 1R4A GNP 8.48485
92 3KUD GDP 8.64198
93 3Q85 GNP 8.87574
94 2HT6 GDP 9.1954
95 2C5L GTP 9.24856
96 5E95 GDP 9.27835
97 2EFE GNH 9.39227
98 1G16 GDP 9.41177
99 2EW1 GNP 9.45274
100 4DCT GDP 9.49555
101 3Q72 GNP 9.63855
102 3GJ8 GDP 9.78261
103 5W75 GDP 9.79228
104 2QN6 GDP 10.089
105 1KSH GDP 10.089
106 1S9D GDP 10.3448
107 4BAS GNP 10.5528
108 3DOE GTP 10.6825
109 3GJ7 GDP 11.2245
110 2W83 GTP 11.6883
111 3CPJ GDP 13.3531
112 5EE5 GTP 14.5401
113 2A9K GDP 14.9733
114 1UAD GNP 16
115 1U8Z GDP 16.6667
116 1O3Y GTP 18.0723
117 5O2T GSP 18.9349
118 3VMF GTP 19.8813
119 3WXM GTP 19.8813
120 3CH5 GDP 21.1538
121 1ZC3 GNP 22.2857
122 5OEC GDP 23.4973
123 1Z0K GTP 33.3333
Pocket No.: 2; Query (leader) PDB : 4LC1; 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: 4lc1.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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