Receptor
PDB id Resolution Class Description Source Keywords
1VJ7 2.1 Å EC: 3.1.7.2 CRYSTAL STRUCTURE OF THE BIFUNCTIONAL CATALYTIC FRAGMENT OF THE RELA/SPOT HOMOLOG FROM STREPTOCOCCUS EQUISIMILIS. STREPTOCOCCUS DYSGALACTIAE SUBSP. EQUIORGANISM_TAXID: 119602 HD DOMAIN ALPHA BETA 2-LAYER SANDWICH HELIX BUNDLE MANGANPPG2-prime :3-prime P (P)PPGPP PPGPP RELA SPOT STRINGENT RESPONSESTRINGENT FACTOR STRINGENT EFFECTOR MAGIC SPOT RSH HYDRTRANSFERASE
Ref.: CONFORMATIONAL ANTAGONISM BETWEEN OPPOSING ACTIVE S BIFUNCTIONAL RELA/SPOT HOMOLOG MODULATES (P)PPGPP M DURING THE STRINGENT RESPONSE. CELL(CAMBRIDGE,MASS.) V. 117 57 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:998;
B:1998;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
GPX B:1999;
Valid;
none;
submit data
505.165 C10 H14 N5 O13 P3 c1nc2...
MN A:997;
B:1997;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1VJ7 2.1 Å EC: 3.1.7.2 CRYSTAL STRUCTURE OF THE BIFUNCTIONAL CATALYTIC FRAGMENT OF THE RELA/SPOT HOMOLOG FROM STREPTOCOCCUS EQUISIMILIS. STREPTOCOCCUS DYSGALACTIAE SUBSP. EQUIORGANISM_TAXID: 119602 HD DOMAIN ALPHA BETA 2-LAYER SANDWICH HELIX BUNDLE MANGANPPG2-prime :3-prime P (P)PPGPP PPGPP RELA SPOT STRINGENT RESPONSESTRINGENT FACTOR STRINGENT EFFECTOR MAGIC SPOT RSH HYDRTRANSFERASE
Ref.: CONFORMATIONAL ANTAGONISM BETWEEN OPPOSING ACTIVE S BIFUNCTIONAL RELA/SPOT HOMOLOG MODULATES (P)PPGPP M DURING THE STRINGENT RESPONSE. CELL(CAMBRIDGE,MASS.) V. 117 57 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1VJ7 - GPX C10 H14 N5 O13 P3 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1VJ7 - GPX C10 H14 N5 O13 P3 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1VJ7 - GPX C10 H14 N5 O13 P3 c1nc2c(n1[....
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: GPX; Similar ligands found: 87
No: Ligand ECFP6 Tc MDL keys Tc
1 GPX 1 1
2 GDP 0.634409 0.946667
3 UCG 0.632479 0.910256
4 G3D 0.602041 0.959459
5 G4P 0.59 0.959459
6 GTP 0.581633 0.946667
7 DGI 0.56701 0.922078
8 SGP 0.56383 0.871795
9 GP3 0.556701 0.922078
10 GNH 0.545455 0.934211
11 GNP 0.539216 0.922078
12 9GM 0.539216 0.922078
13 0O2 0.537736 0.959459
14 GH3 0.533981 0.946667
15 G 0.53125 0.933333
16 P2G 0.53125 0.932432
17 5GP 0.53125 0.933333
18 G1R 0.529412 0.934211
19 GCP 0.529412 0.922078
20 GAV 0.528846 0.910256
21 GSP 0.524272 0.898734
22 P1G 0.520408 0.92
23 Y9Z 0.518182 0.855422
24 DGT 0.514563 0.922078
25 G2R 0.514019 0.910256
26 G2P 0.509615 0.910256
27 GMV 0.504854 0.922078
28 BGO 0.495798 0.898734
29 GPG 0.495413 0.910256
30 2GP 0.494845 0.959459
31 3GP 0.494845 0.92
32 GDD 0.491071 0.910256
33 GKE 0.491071 0.910256
34 GDC 0.491071 0.910256
35 ALF 5GP 0.490385 0.841463
36 GP2 0.490196 0.910256
37 GTG 0.486726 0.8875
38 6CK 0.482456 0.8875
39 G5P 0.478261 0.922078
40 GMP 0.478261 0.828947
41 GDP ALF 0.477064 0.841463
42 ALF GDP 0.477064 0.841463
43 GDR 0.473684 0.910256
44 GFB 0.473684 0.910256
45 G3A 0.469565 0.922078
46 GDP AF3 0.463636 0.841463
47 GKD 0.461538 0.910256
48 JB2 0.461538 0.910256
49 DG 0.46 0.909091
50 DGP 0.46 0.909091
51 GDX 0.457627 0.922078
52 GPD 0.457627 0.876543
53 YGP 0.45614 0.853659
54 GGZ 0.453704 0.804878
55 LQJ 0.452174 0.844156
56 PCG 0.451923 0.906667
57 35G 0.451923 0.906667
58 C2E 0.451923 0.894737
59 GCP G 0.451327 0.894737
60 FEG 0.447154 0.833333
61 U2G 0.447154 0.8875
62 NGD 0.447154 0.910256
63 GDP 7MG 0.440678 0.8625
64 CG2 0.44 0.8875
65 JB3 0.439024 0.898734
66 2MD 0.436508 0.845238
67 GGM 0.436508 0.876543
68 G G 0.435897 0.897436
69 ZGP 0.432 0.823529
70 G1G 0.430769 0.876543
71 TPG 0.428571 0.797753
72 CAG 0.426357 0.835294
73 MD1 0.424242 0.845238
74 5GP 5GP 0.420561 0.857143
75 DG DG 0.417391 0.841463
76 KB7 0.416667 0.780488
77 MGD 0.415385 0.845238
78 GPC 0.415385 0.833333
79 PGD 0.413534 0.876543
80 G U 0.409449 0.851852
81 1YC 0.408333 0.918919
82 DBG 0.407407 0.898734
83 KBD 0.405172 0.780488
84 G C 0.403101 0.851852
85 IDP 0.401869 0.92
86 AKW 0.401575 0.843373
87 G A A A 0.4 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VJ7; 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: 1vj7.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1VJ7; 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: 1vj7.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1VJ7; Ligand: GPX; 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: 1vj7.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
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