Receptor
PDB id Resolution Class Description Source Keywords
2ZGY 1.9 Å NON-ENZYME: MOBILE PARM WITH GDP ESCHERICHIA COLI PARM PLASMID PLASMID PARTITION STRUCTURAL PROTEIN
Ref.: MOLECULAR STRUCTURE OF THE PARM POLYMER AND THE MECHANISM LEADING TO ITS NUCLEOTIDE-DRIVEN DYNAMIC INSTABILITY EMBO J. V. 27 570 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:323;
B:323;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:321;
A:322;
B:321;
B:322;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2ZGY 1.9 Å NON-ENZYME: MOBILE PARM WITH GDP ESCHERICHIA COLI PARM PLASMID PLASMID PARTITION STRUCTURAL PROTEIN
Ref.: MOLECULAR STRUCTURE OF THE PARM POLYMER AND THE MECHANISM LEADING TO ITS NUCLEOTIDE-DRIVEN DYNAMIC INSTABILITY EMBO J. V. 27 570 2008
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 61 families.
1 4A61 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 2ZGY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1MWM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2ZGZ - GNP C10 H17 N6 O13 P3 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 55 families.
1 4A61 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 2ZGY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1MWM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2ZGZ - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 39 families.
1 4A61 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 2ZGY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 1MWM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2ZGZ - GNP C10 H17 N6 O13 P3 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 : 2ZGY; Ligand: GDP; Similar sites found: 61
This union binding pocket(no: 1) in the query (biounit: 2zgy.bio3) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4GNI ATP 0.0000001727 0.57909 2.1875
2 4ZLU 4PW 0.00004789 0.51997 2.1875
3 4ZLU ADP 0.00004789 0.51997 2.1875
4 1TV5 ORO 0.01651 0.41132 2.5
5 4A2B AGS 0.0000001273 0.60977 2.8125
6 4A2A ATP 0.0000001633 0.6021 2.8125
7 2QXL ATP 0.0000002291 0.59576 3.125
8 4JNE ATP 0.000007418 0.5401 3.125
9 4B9Q ATP 0.00001124 0.52524 3.125
10 4BR5 ANP 0.00007993 0.50828 3.125
11 4YDU ADP 0.005895 0.40877 3.37553
12 2IVN ANP 0.002713 0.42853 3.4375
13 3BF1 ADP 0.0004584 0.45728 3.61446
14 4EHU ANP 0.00000005507 0.63137 3.62319
15 5F1X ATP 0.0000001452 0.62731 3.75
16 4A59 AMP 0.0008479 0.44166 3.75
17 2YHW BM3 0.004598 0.42403 3.75
18 5EOB 5QQ 0.02837 0.40631 3.76176
19 4BGB ADP 0.000115 0.44942 4.0625
20 2D0O ADP 0.00003736 0.47996 4.8
21 3WQT ANP 0.0000009602 0.57165 5.3125
22 2W41 ADP 0.001168 0.41284 5.52268
23 2UYT LRH 0.000008097 0.4492 5.9375
24 2UYT ADP 0.000008097 0.4492 5.9375
25 3GDQ ADP 0.000001654 0.58699 6.875
26 5AR0 GB8 0.0000009085 0.57536 6.875
27 5FPE 3TR 0.000008772 0.51371 6.875
28 2FF3 ATP 0.000000667 0.57572 7.1875
29 3QFU ADP 0.0000004938 0.57033 7.1875
30 1T44 ATP 0.000001144 0.56561 7.1875
31 2FF6 ATP 0.000001334 0.56271 7.1875
32 4H03 ATP 0.000001206 0.47241 7.1875
33 4H03 LAR 0.000001328 0.46524 7.1875
34 5EYP GDP 0.009059 0.40806 7.1875
35 2WTX VDO 0.0199 0.40178 8.125
36 5EOU ATP 0.0000001222 0.61055 8.60215
37 2BUP ATP 0.00000003331 0.64096 9.375
38 2BUP ADP 0.00000003331 0.64096 9.375
39 4MO4 ACP 0.0007567 0.45946 9.375
40 3VET TOY 0.02041 0.41872 9.6875
41 3VET CP 0.01895 0.41483 9.6875
42 3VET ADP 0.01895 0.41483 9.6875
43 5M45 AMP 0.001864 0.4155 10.119
44 4CZG ADP 0.0000000801 0.64729 10.3125
45 4CZG QH3 0.00000008823 0.64729 10.3125
46 2GMH FAD 0.02425 0.40739 10.3125
47 3VGL ANP 0.0001984 0.45493 10.625
48 2A40 ATP 0.0000003767 0.58643 11.1538
49 2A42 ATP 0.0000004458 0.58327 11.1538
50 2A3Z ATP 0.0000005181 0.58045 11.1538
51 2D1K ATP 0.0000007472 0.57359 11.1538
52 3LDQ 3P1 0.00006581 0.4896 11.4035
53 3RYC GTP 0.009173 0.4117 12.5874
54 5HTX ADP 0.000662 0.42138 12.8125
55 2V7Y ADP 0.0000003536 0.57634 17.5
56 4LNU GTP 0.01168 0.40172 18.3432
57 2QWO ADP 0.0000004756 0.59025 18.4783
58 3ZEU AGS 0.001121 0.43841 19.9134
59 3ZEU ADP 0.002465 0.41965 19.9134
60 3AAQ ARU 0.00051 0.47545 23.125
61 2YCH ATP 0.0000001245 0.61307 26.875
Pocket No.: 2; Query (leader) PDB : 2ZGY; Ligand: GDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2zgy.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2ZGY; Ligand: GDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2zgy.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2ZGY; Ligand: GDP; Similar sites found: 2
This union binding pocket(no: 4) in the query (biounit: 2zgy.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4L50 D8X 0.01387 0.40106 2.63158
2 2WTX UDP 0.01474 0.4068 8.125
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