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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...
View in 3D viewer
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 65 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 56 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: 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 : 2ZGY; Ligand: GDP; Similar sites found with APoc: 113
This union binding pocket(no: 1) in the query (biounit: 2zgy.bio3) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2CZL TLA 1.10294
2 5N9X THR 1.5625
3 3WXL ADP 1.875
4 5DO8 BGC 1.875
5 4Y9T PA1 1.875
6 5C9P FUC 1.875
7 1SQ5 ADP 1.94805
8 2I7C AAT 2.12014
9 4GNI ATP 2.1875
10 4ZLU 4PW 2.1875
11 4ZLU ADP 2.1875
12 5ZI9 FLC 2.30769
13 3LL5 IP8 2.40964
14 1TV5 ORO 2.5
15 3ITJ CIT 2.5
16 6F5W KG1 2.5
17 1YNS HPO 2.68199
18 4A2A ATP 2.8125
19 4A2B AGS 2.8125
20 3F8D FAD 2.8125
21 4K7O EKZ 2.8125
22 4O08 PO6 2.8125
23 5E5U MLI 3.01508
24 2QXL ATP 3.125
25 4B9Q ATP 3.125
26 4BR5 ANP 3.125
27 4JNE ATP 3.125
28 5KJW 53C 3.125
29 4YDU ADP 3.37553
30 5OBY ANP 3.4375
31 5OBU ANP 3.4375
32 6EOF ADP 3.4375
33 2IVN ANP 3.4375
34 6C0B PAM 3.4375
35 3BF1 ADP 3.61446
36 2WPB ZZI 3.61842
37 4EHU ANP 3.62319
38 6ASY ATP 3.75
39 5EXW 7DT 3.75
40 4A59 AMP 3.75
41 5EOB 5QQ 3.76176
42 4WGF HX2 3.90244
43 5A96 GTP 4.01606
44 4BGB ADP 4.0625
45 4UOX PLP 4.0625
46 2VAR AMP 4.15335
47 1H74 ILE 4.39189
48 1TKU 5RP 4.41176
49 2D0O ADP 4.8
50 1WHT BZS 5.07812
51 3ENG CBI 5.16432
52 3WQT ANP 5.3125
53 3A23 GAL 5.3125
54 6BVJ EAS 5.38922
55 4URX FK1 5.40541
56 6ACS CIT 5.42636
57 2W41 ADP 5.52268
58 2BTO GTP 5.625
59 1ZEI CRS 5.66038
60 3I9U DTU 5.70342
61 2UYT ADP 5.9375
62 2UYT LRH 5.9375
63 6BVI EC4 6.58683
64 6BVL EBY 6.58683
65 5JIC N7E 6.59341
66 5JIC ADP 6.59341
67 5AR0 GB8 6.875
68 5FPE 3TR 6.875
69 5W3Y ACO 6.875
70 3QFU ADP 7.1875
71 2FF3 ATP 7.1875
72 6G3R ADP 7.1875
73 2FF6 ATP 7.1875
74 4H03 ATP 7.1875
75 4H03 LAR 7.1875
76 5EYP GDP 7.1875
77 2WTX VDO 8.125
78 5EOU ATP 8.60215
79 2E2P ADP 9.0301
80 2BUP ADP 9.375
81 2BUP ATP 9.375
82 4MO4 ACP 9.375
83 3VET TOY 9.6875
84 3VET ADP 9.6875
85 3VET CP 9.6875
86 5EIB GTP 9.6875
87 1YRO UDP 9.79021
88 5M45 AMP 10.119
89 4CZG ADP 10.3125
90 4CZG QH3 10.3125
91 2GMH FAD 10.3125
92 3VGL ANP 10.625
93 5XQL C2E 10.9375
94 2D1K ATP 11.1538
95 2A40 ATP 11.1538
96 2A42 ATP 11.1538
97 2A3Z ATP 11.1538
98 3LDQ 3P1 11.4035
99 1L5Y BEF 11.6129
100 2FMD MAN MAN 11.6667
101 3RYC GTP 12.5874
102 5HTX ADP 12.8125
103 6B3V 7DQ 13.75
104 6B3V ANP 13.75
105 2O07 MTA 14.1447
106 2O07 SPD 14.1447
107 5TQZ GLC 15.3333
108 5ZZA ATP 16.5289
109 2V7Y ADP 17.5
110 4LNU GTP 18.3432
111 2QWO ADP 18.4783
112 3AAQ ARU 23.125
113 2YCH ATP 26.875
Pocket No.: 2; Query (leader) PDB : 2ZGY; 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: 2zgy.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2ZGY; Ligand: GDP; Similar sites found with APoc: 27
This union binding pocket(no: 3) in the query (biounit: 2zgy.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3IB1 IMN 1.25
2 2EB5 OXL 1.49813
3 5HV7 RBL 2.1875
4 2ZUX RAM 2.5
5 1SQS TLA 2.5
6 4L50 D8X 2.63158
7 1BZL GCG 2.8125
8 1FNZ A2G 2.95359
9 3BZ3 YAM 3.26087
10 1T9D P22 3.75
11 4IV9 TSR 4.0625
12 5MB4 NAG 4.0625
13 5JIB OIA 4.0625
14 1D1Q 4NP 4.34783
15 4USI AKG 4.54545
16 5M6N 7H9 5.08475
17 2WTX UDP 8.125
18 1KUJ MMA 8.27068
19 1WS4 GYP 9.02256
20 1UGW GAL 9.02256
21 1WS5 MMA 9.02256
22 3BY9 SIN 9.0625
23 1TOQ AMG 9.77444
24 1DL5 SAH 11.041
25 4CP8 MLI 12.8125
26 4JZ8 CIT 12.9338
27 6BJO DUY 16
Pocket No.: 4; Query (leader) PDB : 2ZGY; 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: 4) in the query (biounit: 2zgy.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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