Receptor
PDB id Resolution Class Description Source Keywords
3MD0 2.45 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF ARGININE/ORNITHINE TRANSPORT SYSTEM ATP MYCOBACTERIUM TUBERCULOSIS BOUND TO GDP (A RAS-LIKE GTPASE S UPERFAMILY PROTEIN) MYCOBACTERIUM TUBERCULOSIS SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE RLIKE GTPASE ALLOSTERIC MODULATOR TUBERCULOSIS ATP-BINDINNUCLEOTIDE-BINDING SSGCID TRANSPORT PROTEIN
Ref.: CRYSTAL STRUCTURES OF MYCOBACTERIAL MEAB AND MMAA-L GTPASES. J.STRUCT.FUNCT.GENOM. V. 16 91 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:335;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
UNX A:336;
A:337;
A:338;
A:339;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
n/a X *
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3MD0 2.45 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF ARGININE/ORNITHINE TRANSPORT SYSTEM ATP MYCOBACTERIUM TUBERCULOSIS BOUND TO GDP (A RAS-LIKE GTPASE S UPERFAMILY PROTEIN) MYCOBACTERIUM TUBERCULOSIS SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE RLIKE GTPASE ALLOSTERIC MODULATOR TUBERCULOSIS ATP-BINDINNUCLEOTIDE-BINDING SSGCID TRANSPORT PROTEIN
Ref.: CRYSTAL STRUCTURES OF MYCOBACTERIAL MEAB AND MMAA-L GTPASES. J.STRUCT.FUNCT.GENOM. V. 16 91 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 3MD0 - 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 209 families.
1 3MD0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 3TK1 - 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 : 3MD0; Ligand: GDP; Similar sites found with APoc: 129
This union binding pocket(no: 1) in the query (biounit: 3md0.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1DAR GDP 1.69014
2 1RYH GNP 1.97044
3 1KK1 GNP 1.97183
4 2QTV GNP 1.97183
5 3CX8 GSP 2.07101
6 1MH1 GNP 2.15054
7 5CK5 GDP 2.21519
8 4J0Q GDP 2.25352
9 6AU6 GDP 2.25352
10 1CS4 GSP 2.25352
11 1YRB GDP 2.29008
12 4YLG GDP 2.89017
13 1G7S GDP 3.09859
14 1TQ4 GDP 3.09859
15 5OEC GDP 3.27869
16 1D2E GDP 3.38028
17 3VMF GTP 3.38028
18 5FG3 GDP 3.38028
19 5YT0 GDP 3.38028
20 3WXM GTP 3.38028
21 3WY9 GDP 3.66197
22 5M04 GDP 3.66197
23 1SKQ GDP 3.66197
24 3WYA GDP 3.66197
25 2AWN ADP 3.66197
26 1VG1 GDP 3.78378
27 1VG9 GDP 3.78378
28 1Y3A GDP 3.95137
29 1BH2 GSP 4.12698
30 2A5J GDP 4.18848
31 4B47 GDP 4.22535
32 3DOE GTP 4.24242
33 1FZQ GDP 4.41989
34 1MKY GDP 4.50704
35 1PUJ GNP 4.60993
36 5W7Q GDP 4.78873
37 2C78 GNP 5.07042
38 5W75 GDP 5.07042
39 1KSH GDP 5.26316
40 5TB5 GDP 5.33333
41 1Z2A GDP 5.35714
42 3GJ8 GDP 5.42986
43 3GJ3 GDP 5.42986
44 3GJ4 GDP 5.42986
45 3GJ5 GDP 5.42986
46 3WYF GTP 5.47945
47 3M1I GTP 5.47945
48 3T5G GDP 5.52486
49 1Z0F GDP 5.58659
50 5W76 GDP 5.6338
51 2CJW GDP 5.72917
52 1OIV GDP 5.75916
53 5GOE GDP 5.91549
54 4DKX GDP 6.01852
55 3T1O GDP 6.06061
56 5H7J GCP 6.19718
57 5UWP GNP 6.29371
58 5UWU GNP 6.29371
59 6CIT GNP 6.29371
60 5UWQ GNP 6.29371
61 5UWW GNP 6.29371
62 5DHF GNP 6.29371
63 5UWO GNP 6.29371
64 5UWS GNP 6.29371
65 5UWH GNP 6.29371
66 5UWT GNP 6.29371
67 1Z0A GDP 6.32184
68 1ZJ6 G3D 6.41711
69 4HAT GNP 6.42857
70 3Q85 GNP 6.50888
71 3T12 GDP ALF 6.61765
72 5KDO GDP 6.76056
73 1WA5 GTP 6.81818
74 2WJG GDP 6.91489
75 5EE5 GTP 7.01754
76 1S9D GDP 7.04225
77 1RE0 GDP 7.04225
78 1D8T GDP 7.04225
79 5XKT GNP 7.04225
80 1MR3 G3D 7.18232
81 1YZG GDP 7.26257
82 1R4A GNP 7.27273
83 5HCN GCP 7.27969
84 2HCJ GDP 7.46269
85 1F6B GDP 7.57576
86 2FFQ GSP 7.60234
87 4G5G GDP 7.60563
88 3U6B GDP 7.60563
89 4P3Y GDP 7.60563
90 5JBQ GDP 7.60563
91 3U6K GDP 7.60563
92 4PC3 GDP 7.60563
93 1Z0J GTP 7.64706
94 1YVD GNP 7.69231
95 2WJH GDP 7.83133
96 3Q72 GNP 7.83133
97 6CRK GDP 7.88732
98 5H7K GDP 7.88732
99 3WYG GTP 7.89474
100 2HT6 GDP 8.04598
101 2RCN GDP 8.16901
102 1G16 GDP 8.23529
103 3SFV GDP 8.28729
104 2EFE GNH 8.28729
105 5O74 GDP 8.33333
106 4HDO GNP 8.38323
107 4DCT GDP 8.4507
108 3RWO GDP 8.64865
109 3CNL GNP 8.73239
110 5JCZ GDP 8.93855
111 1UAD GNP 9.14286
112 2QN6 GDP 9.29577
113 1U8Z GDP 9.52381
114 1S8F GDP 10.1695
115 1CLU DBG 10.241
116 3AQ4 GDP 10.8696
117 2C5L GTP 11.1111
118 3GJ7 GDP 11.2245
119 5WDR GNP 11.6959
120 3N5C GDP 11.7284
121 1J2J GTP 12.0482
122 1GUA GNP 12.3457
123 3CPJ GDP 13.8028
124 5E95 GDP 14.433
125 3CH5 GDP 21.1538
126 3BC1 GNP 23.7288
127 2OM2 GDP 25
128 2W83 GTP 29.8701
129 4HI0 GDP 33.1658
Pocket No.: 2; Query (leader) PDB : 3MD0; 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: 3md0.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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