Receptor
PDB id Resolution Class Description Source Keywords
1NHT 2.5 Å EC: 6.3.4.4 ENTRAPMENT OF 6-THIOPHOSPHORYL-IMP IN THE ACTIVE SITE OF CRY ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI DATA COLL1 00K ESCHERICHIA COLI LIGASE SYNTHETASE PURINE NUCLEOTIDE BIOSYNTHESIS GTP-HYDRENZYMES
Ref.: ENTRAPMENT OF 6-THIOPHOSPHORYL-IMP IN THE ACTIVE SI CRYSTALLINE ADENYLOSUCCINATE SYNTHETASE FROM ESCHER COLI. J.BIOL.CHEM. V. 272 15200 1997
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:432;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
HDA A:437;
Valid;
none;
submit data
119.076 C3 H5 N O4 C(C(=...
MG A:435;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
PGS A:440;
Valid;
none;
submit data
445.259 C10 H15 N4 O10 P2 S c1[nH...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1QF5 2 Å EC: 6.3.4.4 DESIGN, SYNTHESIS, AND X-RAY CRYSTAL STRUCTURE OF AN ENZYME BISUBSTRATE HYBRID INHIBITOR OF ADENYLOSUCCINATE SYNTHETASE ESCHERICHIA COLI PURINE BIOSYNTHESIS SYNTHETASE GTP-BINDING GTP-HYDROLYSINENZYMES LIGASE
Ref.: AN ENZYME-BOUND BISUBSTRATE HYBRID INHIBITOR OF ADENYLOSUCCINATE SYNTHETASE ANGEW.CHEM.INT.ED.ENGL. V. 38 3159 1999
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1HOO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 1NHT - HDA C3 H5 N O4 C(C(=O)O)N....
3 1GIM - HDA C3 H5 N O4 C(C(=O)O)N....
4 1CIB - HDA C3 H5 N O4 C(C(=O)O)N....
5 1QF4 ic50 = 0.665 uM RPD C13 H22 N3 O13 P C(C[C@H](C....
6 1CH8 - HDA C3 H5 N O4 C(C(=O)O)N....
7 1CG0 - HDA C3 H5 N O4 C(C(=O)O)N....
8 1CG1 - HDA C3 H5 N O4 C(C(=O)O)N....
9 2GCQ Ki = 17 uM HDA C3 H5 N O4 C(C(=O)O)N....
10 1HON - GNH C10 H16 N6 O10 P2 c1nc2c(n1[....
11 1CG4 - IMO C10 H14 N4 O11 P2 c1nc2c(c(n....
12 1CG3 - HDA C3 H5 N O4 C(C(=O)O)N....
13 1QF5 ic50 = 0.043 uM RPL C13 H22 N3 O13 P C(C[C@@H](....
14 1HOP - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1HOO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 1NHT - HDA C3 H5 N O4 C(C(=O)O)N....
3 1GIM - HDA C3 H5 N O4 C(C(=O)O)N....
4 1CIB - HDA C3 H5 N O4 C(C(=O)O)N....
5 1QF4 ic50 = 0.665 uM RPD C13 H22 N3 O13 P C(C[C@H](C....
6 1CH8 - HDA C3 H5 N O4 C(C(=O)O)N....
7 1CG0 - HDA C3 H5 N O4 C(C(=O)O)N....
8 1CG1 - HDA C3 H5 N O4 C(C(=O)O)N....
9 2GCQ Ki = 17 uM HDA C3 H5 N O4 C(C(=O)O)N....
10 1HON - GNH C10 H16 N6 O10 P2 c1nc2c(n1[....
11 1CG4 - IMO C10 H14 N4 O11 P2 c1nc2c(c(n....
12 1CG3 - HDA C3 H5 N O4 C(C(=O)O)N....
13 1QF5 ic50 = 0.043 uM RPL C13 H22 N3 O13 P C(C[C@@H](....
14 1HOP - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
50% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1HOO - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
2 1NHT - HDA C3 H5 N O4 C(C(=O)O)N....
3 1GIM - HDA C3 H5 N O4 C(C(=O)O)N....
4 1CIB - HDA C3 H5 N O4 C(C(=O)O)N....
5 1QF4 ic50 = 0.665 uM RPD C13 H22 N3 O13 P C(C[C@H](C....
6 1CH8 - HDA C3 H5 N O4 C(C(=O)O)N....
7 1CG0 - HDA C3 H5 N O4 C(C(=O)O)N....
8 1CG1 - HDA C3 H5 N O4 C(C(=O)O)N....
9 2GCQ Ki = 17 uM HDA C3 H5 N O4 C(C(=O)O)N....
10 1HON - GNH C10 H16 N6 O10 P2 c1nc2c(n1[....
11 1CG4 - IMO C10 H14 N4 O11 P2 c1nc2c(c(n....
12 1CG3 - HDA C3 H5 N O4 C(C(=O)O)N....
13 1QF5 ic50 = 0.043 uM RPL C13 H22 N3 O13 P C(C[C@@H](....
14 1HOP - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
15 5I34 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 1P9B - HDA C3 H5 N O4 C(C(=O)O)N....
17 1IWE - IMP C10 H13 N4 O8 P c1nc2c(n1[....
18 1LON - HDA C3 H5 N O4 C(C(=O)O)N....
19 1MF0 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
20 2DGN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 1LOO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
22 1MEZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
23 1LNY - IMO C10 H14 N4 O11 P2 c1nc2c(c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 168
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 9GM 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 GKE 0.747253 0.961039
18 GDD 0.747253 0.961039
19 GDC 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 GDR 0.72043 0.961039
26 GFB 0.72043 0.961039
27 GTG 0.72043 0.936709
28 G4P 0.715909 0.986486
29 6CK 0.712766 0.936709
30 G3A 0.712766 0.973684
31 GDP AF3 0.7 0.888889
32 GDP ALF 0.7 0.888889
33 ALF GDP 0.7 0.888889
34 YGP 0.698925 0.901235
35 JB2 0.697917 0.961039
36 GKD 0.697917 0.961039
37 GPD 0.690722 0.925
38 GDX 0.690722 0.973684
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 GDP 7MG 0.636364 0.911392
44 DGI 0.636364 0.923077
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 KB7 0.629214 0.82716
52 CG2 0.622642 0.936709
53 FEG 0.619048 0.879518
54 MGD 0.614679 0.891566
55 ZGP 0.613208 0.869048
56 GH3 0.612903 0.973333
57 3GP 0.611765 0.946667
58 MD1 0.607143 0.891566
59 PGD 0.59292 0.925
60 DGT 0.591398 0.923077
61 BGO 0.588785 0.924051
62 TPG 0.582609 0.840909
63 DBG 0.582609 0.948718
64 KBD 0.581633 0.82716
65 2GP 0.574713 0.96
66 FE9 0.570175 0.776596
67 GCP G 0.56 0.921053
68 KBJ 0.558824 0.797619
69 G A A A 0.553571 0.923077
70 A G 0.553571 0.935065
71 MGP 0.553191 0.961039
72 U A G G 0.548673 0.935065
73 G4M 0.548387 0.880952
74 6G0 0.547368 0.961039
75 G1R G1R 0.542373 0.924051
76 P2G 0.527473 0.883117
77 PGD O 0.525 0.850575
78 ADP 0.522222 0.92
79 R5I 0.520833 0.946667
80 R7I 0.520833 0.946667
81 GGM 0.517544 0.901235
82 DGP 0.516484 0.910256
83 DG 0.516484 0.910256
84 P1G 0.516129 0.871795
85 G U 0.513274 0.9
86 G1G 0.508475 0.925
87 IMP 0.505495 0.959459
88 AKW 0.504425 0.890244
89 G C 0.504348 0.9
90 GPC 0.491525 0.879518
91 G7M 0.483871 0.948052
92 6AD 0.479592 0.841463
93 ATP 0.473684 0.92
94 HEJ 0.473684 0.92
95 G2Q 0.471154 0.961039
96 AQP 0.46875 0.92
97 5FA 0.46875 0.92
98 GTA 0.468468 0.936709
99 7DD 0.468085 0.906667
100 G G G RPC 0.466102 0.875
101 SGP 0.463158 0.82716
102 01G 0.462963 0.902439
103 JSQ 0.459184 0.873418
104 HFD 0.459184 0.873418
105 AP5 0.457447 0.894737
106 B4P 0.457447 0.894737
107 A2D 0.456522 0.894737
108 6YZ 0.455446 0.896104
109 G G G C 0.455285 0.9125
110 ANP 0.454545 0.896104
111 5GP 5GP 0.454545 0.883117
112 ACQ 0.454545 0.896104
113 AT4 0.452632 0.884615
114 A G C C 0.451613 0.911392
115 APC G U 0.45082 0.886076
116 PRT 0.449541 0.959459
117 G U34 0.449153 0.888889
118 DG DG 0.448598 0.865854
119 ITT 0.447917 0.868421
120 BA3 0.446809 0.894737
121 35G 0.444444 0.933333
122 PCG 0.444444 0.933333
123 C2E 0.444444 0.921053
124 MGO 0.441176 0.864198
125 AN2 0.4375 0.907895
126 G C C C 0.4375 0.924051
127 NO7 0.436893 0.860759
128 M33 0.43299 0.883117
129 UCG 0.429688 0.911392
130 A G U 0.42963 0.888889
131 ACP 0.428571 0.896104
132 MGQ 0.424528 0.935897
133 7DT 0.424242 0.906667
134 APR 0.424242 0.894737
135 AR6 0.424242 0.894737
136 93A 0.42268 0.833333
137 A4P 0.420168 0.869048
138 AGS 0.42 0.873418
139 AD9 0.42 0.896104
140 G8D 0.42 0.875
141 SAP 0.42 0.873418
142 CA0 0.418367 0.896104
143 ATF 0.417476 0.884615
144 AGO 0.414634 0.888889
145 A G U U 0.414286 0.888889
146 KG4 0.414141 0.896104
147 NIA 0.413043 0.82716
148 MGV 0.412844 0.890244
149 T99 0.411765 0.884615
150 TAT 0.411765 0.884615
151 A1R 0.411215 0.839506
152 ADQ 0.411215 0.871795
153 RGT 0.410714 0.909091
154 CGP 0.409836 0.86747
155 HQG 0.409524 0.907895
156 C1Z 0.409091 0.986486
157 AMP 0.408602 0.893333
158 A 0.408602 0.893333
159 UP5 0.40678 0.873418
160 C2R 0.406593 0.906667
161 AMZ 0.406593 0.918919
162 JBT 0.405882 0.778947
163 A22 0.40566 0.907895
164 25L 0.405405 0.907895
165 ADX 0.40404 0.809524
166 8OD 0.401961 0.946667
167 4TC 0.4 0.851852
168 50T 0.4 0.883117
Ligand no: 2; Ligand: HDA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 HDA 1 1
Ligand no: 3; Ligand: PGS; Similar ligands found: 123
No: Ligand ECFP6 Tc MDL keys Tc
1 PGS 1 1
2 AMP 0.575 0.857143
3 A 0.575 0.857143
4 IMO 0.554217 0.868421
5 6MZ 0.547619 0.846154
6 71V 0.523256 0.923077
7 6IA 0.51087 0.767442
8 2SA 0.5 0.85
9 6C6 0.5 0.804878
10 ADX 0.488889 0.821429
11 7RP 0.488372 0.866667
12 ADP 0.483146 0.883117
13 7RA 0.482759 0.846154
14 A2D 0.482759 0.858974
15 45A 0.482759 0.8125
16 RMB 0.482759 0.815789
17 ABM 0.482759 0.8125
18 P2P 0.482759 0.844156
19 25A 0.479592 0.858974
20 SRA 0.476744 0.884615
21 AIR 0.475 0.794872
22 ITT 0.472527 0.881579
23 M33 0.472527 0.848101
24 BA3 0.47191 0.858974
25 A12 0.47191 0.85
26 AP2 0.47191 0.85
27 PMO 0.47191 0.794872
28 N6P 0.47 0.855263
29 HEJ 0.467391 0.883117
30 ATP 0.467391 0.883117
31 B4P 0.466667 0.858974
32 AP5 0.466667 0.858974
33 1RB 0.465116 0.826667
34 6K6 0.464646 0.846154
35 C2R 0.464286 0.8
36 AMZ 0.464286 0.810127
37 5FA 0.462366 0.883117
38 APC 0.462366 0.85
39 AQP 0.462366 0.883117
40 AN2 0.461538 0.871795
41 AT4 0.461538 0.922078
42 RBZ 0.45977 0.794872
43 NO7 0.459184 0.85
44 CA0 0.456522 0.8375
45 AU1 0.456522 0.860759
46 NIA 0.453488 0.752941
47 ACP 0.451613 0.860759
48 50T 0.451613 0.848101
49 KG4 0.451613 0.8375
50 8LH 0.44898 0.804878
51 ACQ 0.447917 0.860759
52 T99 0.447917 0.922078
53 TAT 0.447917 0.922078
54 PRX 0.446809 0.792683
55 AR6 0.446809 0.858974
56 APR 0.446809 0.858974
57 ADP MG 0.445652 0.857143
58 HQG 0.444444 0.871795
59 5AL 0.443299 0.825
60 AD9 0.442105 0.860759
61 AGS 0.442105 0.910256
62 RBY 0.442105 0.82716
63 ADV 0.442105 0.82716
64 SAP 0.442105 0.910256
65 A22 0.44 0.871795
66 8QN 0.435644 0.825
67 SRP 0.434343 0.804878
68 6YZ 0.434343 0.860759
69 FAI 0.433333 0.810127
70 JLN 0.433333 0.810127
71 AAM 0.433333 0.857143
72 ANP 0.43299 0.860759
73 ADQ 0.431373 0.8375
74 PTJ 0.428571 0.797619
75 8LE 0.428571 0.795181
76 ATP MG 0.427083 0.857143
77 ADP PO3 0.427083 0.857143
78 APC MG 0.427083 0.835443
79 8LQ 0.425743 0.804878
80 G 0.425532 0.804878
81 5GP 0.425532 0.804878
82 ATF 0.424242 0.85
83 ADP ALF 0.424242 0.795181
84 ALF ADP 0.424242 0.795181
85 OOB 0.421569 0.825
86 9ZD 0.421569 0.807229
87 9ZA 0.421569 0.807229
88 5SV 0.421569 0.755814
89 IMP 0.419355 0.825
90 GAP 0.418367 0.814815
91 4AD 0.417476 0.839506
92 AMO 0.417476 0.82716
93 PAJ 0.417476 0.788235
94 A3R 0.417476 0.807229
95 ME8 0.415094 0.770115
96 SON 0.414894 0.82716
97 93A 0.414894 0.802326
98 6AD 0.414141 0.924051
99 AHX 0.413462 0.797619
100 00A 0.413462 0.785714
101 MAP 0.411765 0.839506
102 DAL AMP 0.411765 0.825
103 25L 0.411215 0.871795
104 ADP BMA 0.409524 0.8375
105 3UK 0.409524 0.814815
106 A2P 0.408602 0.844156
107 HFD 0.408163 0.839506
108 JSQ 0.408163 0.839506
109 OZV 0.407767 0.858974
110 DTA 0.406977 0.7375
111 AOC 0.406593 0.725
112 VO4 ADP 0.405941 0.848101
113 ADP VO4 0.405941 0.848101
114 LAD 0.40566 0.767442
115 A1R 0.403846 0.807229
116 RGT 0.40367 0.85
117 1ZZ 0.401869 0.75
118 TXA 0.401869 0.82716
119 NB8 0.401869 0.797619
120 FYA 0.401869 0.802469
121 LMS 0.4 0.77907
122 DLL 0.4 0.825
123 ARU 0.4 0.788235
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1QF5; 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: 1) in the query (biounit: 1qf5.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1QF5; 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: 1qf5.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1QF5; Ligand: RPL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1qf5.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1QF5; Ligand: RPL; 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: 1qf5.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
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