Receptor
PDB id Resolution Class Description Source Keywords
2J41 1.9 Å EC: 2.7.4.8 CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS GUANYLATE MONOPHOSPHATE KINASE STAPHYLOCOCCUS AUREUS GMP GMK KINASE TRANSFERASE ATP-BINDING NUCLEOTIDE- BINDING STAPHYLOCOCCUS AUREUS
Ref.: STRUCTURE OF STAPHYLOCOCCUS AUREUS GUANYLATE MONOPHOSPHATE KINASE ACTA CRYSTALLOGR.,SECT.F V. 62 949 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP B:1208;
C:1200;
D:1210;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
363.221 C10 H14 N5 O8 P c1nc2...
K B:1207;
C:1199;
D:1209;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
39.098 K [K+]
SO4 A:1198;
B:1206;
C:1198;
D:1207;
D:1208;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4QRH 1.65 Å EC: 2.7.4.8 MOLECULAR MECHANISM AND EVOLUTION OF GUANYLATE KINASE REGULA (P)PPGPP STAPHYLOCOCCUS AUREUS USA300-ISMMS1 GUANYLATE KINASE PHOSPHOTRANSFERASE PPPGPP TRANSFERASE
Ref.: MOLECULAR MECHANISM AND EVOLUTION OF GUANYLATE KINA REGULATION BY (P)PPGPP. MOL.CELL V. 57 735 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4QRH Ki = 7 uM 0O2 C10 H18 N5 O20 P5 c1nc2c(n1[....
2 2J41 - 5GP C10 H14 N5 O8 P 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 5 families.
1 4QRH Ki = 7 uM 0O2 C10 H18 N5 O20 P5 c1nc2c(n1[....
2 2J41 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1EX7 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 1GKY - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
3 2F3R ic50 = 0.5 uM G5P C20 H29 N10 O23 P5 c1nc(c2c(n....
4 2AN9 - GMP C10 H13 N5 O5 c1nc2c(n1[....
5 1LVG - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 1ZNY - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 1ZNX - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
8 1ZNZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 4QRH Ki = 7 uM 0O2 C10 H18 N5 O20 P5 c1nc2c(n1[....
10 2J41 - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP; Similar ligands found: 165
No: Ligand ECFP6 Tc MDL keys Tc
1 G 1 1
2 5GP 1 1
3 GDP 0.828947 0.986486
4 GP3 0.815789 0.960526
5 GP2 0.805195 0.948052
6 GTP 0.797468 0.986486
7 GNH 0.794872 0.973333
8 G2P 0.777778 0.948052
9 GMV 0.775 0.960526
10 G1R 0.765432 0.973333
11 GCP 0.765432 0.960526
12 GAV 0.759036 0.948052
13 GSP 0.756098 0.935897
14 GNP 0.756098 0.960526
15 9GM 0.756098 0.960526
16 ALF 5GP 0.753086 0.9
17 GMP 0.732394 0.866667
18 GPG 0.724138 0.948052
19 G2R 0.712644 0.948052
20 GDP ALF 0.701149 0.9
21 ALF GDP 0.701149 0.9
22 GDP AF3 0.701149 0.9
23 GKE 0.692308 0.948052
24 Y9Z 0.692308 0.890244
25 GDC 0.692308 0.948052
26 GDD 0.692308 0.948052
27 YGP 0.681319 0.9125
28 G3A 0.677419 0.960526
29 G5P 0.670213 0.960526
30 GTG 0.666667 0.924051
31 KB7 0.666667 0.8375
32 GDR 0.666667 0.948052
33 GFB 0.666667 0.948052
34 6CK 0.659574 0.924051
35 3GP 0.65 0.959459
36 G G 0.648936 0.960526
37 JB2 0.645833 0.948052
38 GKD 0.645833 0.948052
39 GDX 0.639175 0.960526
40 GPD 0.639175 0.9125
41 GDP 7MG 0.635417 0.923077
42 G3D 0.617977 0.972973
43 U2G 0.617647 0.924051
44 KBD 0.612903 0.8375
45 2GP 0.609756 0.946667
46 IMP 0.609756 0.972603
47 JB3 0.607843 0.935897
48 CG2 0.605769 0.924051
49 G4P 0.604396 0.972973
50 DG 0.60241 0.922078
51 DGP 0.60241 0.922078
52 NGD 0.601942 0.948052
53 FEG 0.601942 0.890244
54 ZGP 0.596154 0.879518
55 0O2 0.595745 0.972973
56 KBJ 0.587629 0.807229
57 2MD 0.584906 0.879518
58 G7M 0.583333 0.960526
59 CAG 0.583333 0.869048
60 G A A A 0.579439 0.935065
61 A G 0.579439 0.947368
62 U A G G 0.574074 0.947368
63 MGD 0.568807 0.879518
64 DBG 0.566372 0.935897
65 MD1 0.5625 0.879518
66 PGD 0.5625 0.9125
67 P2G 0.55814 0.894737
68 GCP G 0.556701 0.933333
69 FE9 0.553571 0.784946
70 P1G 0.545455 0.883117
71 GH3 0.542553 0.96
72 TPG 0.53913 0.829545
73 GPX 0.53125 0.933333
74 DGI 0.527473 0.910256
75 G1R G1R 0.525862 0.911392
76 G U 0.522936 0.911392
77 PGD O 0.521368 0.83908
78 DGT 0.521277 0.910256
79 G4M 0.520325 0.869048
80 AKW 0.513761 0.878049
81 G C 0.513514 0.911392
82 93A 0.511364 0.821429
83 IDP 0.505495 0.959459
84 MGQ 0.505155 0.948052
85 C2R 0.5 0.893333
86 AMZ 0.5 0.905405
87 A 0.5 0.905405
88 BGO 0.5 0.911392
89 AMP 0.5 0.905405
90 AIR 0.493671 0.890411
91 MGV 0.49 0.901235
92 SGP 0.488889 0.8375
93 NIA 0.488095 0.8375
94 GPC 0.474138 0.890244
95 G G G RPC 0.473684 0.886076
96 GGM 0.473684 0.888889
97 71V 0.47191 0.85
98 APC G U 0.470085 0.897436
99 MGP 0.46875 0.948052
100 R7I 0.46875 0.933333
101 R5I 0.46875 0.933333
102 C2E 0.468085 0.933333
103 PCG 0.468085 0.945946
104 35G 0.468085 0.945946
105 G1G 0.466102 0.9125
106 RMB 0.465909 0.813333
107 FAI 0.465909 0.905405
108 7RA 0.465909 0.918919
109 AAM 0.465909 0.905405
110 1RB 0.465116 0.824324
111 6G0 0.463918 0.948052
112 5GP 5GP 0.463158 0.894737
113 G G G C 0.462185 0.924051
114 RBZ 0.45977 0.815789
115 UCG 0.459016 0.923077
116 A G C C 0.458333 0.923077
117 DG DG 0.456311 0.876543
118 G U34 0.45614 0.9
119 IMO 0.449438 0.866667
120 A G U 0.446154 0.9
121 6MZ 0.444444 0.868421
122 G C C C 0.443548 0.935897
123 IRN 0.443038 0.808219
124 PMO 0.43956 0.792208
125 7RP 0.438202 0.864865
126 GTA 0.436364 0.924051
127 P2P 0.433333 0.842105
128 JLN 0.433333 0.88
129 A G U U 0.42963 0.9
130 XMP 0.428571 0.907895
131 PGS 0.425532 0.804878
132 RVP 0.423529 0.84
133 G2Q 0.423077 0.948052
134 ADP 0.419355 0.906667
135 45A 0.417582 0.857143
136 A2D 0.417582 0.881579
137 ABM 0.417582 0.857143
138 PRT 0.416667 0.945946
139 GUO 0.415842 0.932432
140 AT4 0.414894 0.871795
141 CA0 0.410526 0.883117
142 2SA 0.41 0.871795
143 1YD 0.409091 0.933333
144 4BW 0.409091 0.933333
145 AP2 0.408602 0.871795
146 A12 0.408602 0.871795
147 BA3 0.408602 0.881579
148 6C6 0.408163 0.825
149 25A 0.407767 0.906667
150 NOS 0.406977 0.813333
151 KG4 0.40625 0.883117
152 HEJ 0.40625 0.906667
153 ATP 0.40625 0.906667
154 AP5 0.404255 0.881579
155 B4P 0.404255 0.881579
156 ACQ 0.40404 0.883117
157 ANP 0.40404 0.883117
158 6IA 0.40404 0.785714
159 CGP 0.403361 0.878049
160 5FA 0.402062 0.906667
161 APC 0.402062 0.871795
162 3ZE 0.402062 0.871795
163 AQP 0.402062 0.906667
164 N6P 0.4 0.853333
165 AN2 0.4 0.894737
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4QRH; Ligand: 0O2; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 4qrh.bio2) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1JXM 5GP 42.381
Pocket No.: 2; Query (leader) PDB : 4QRH; Ligand: 0O2; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 4qrh.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1JXM 5GP 42.381
Pocket No.: 3; Query (leader) PDB : 4QRH; Ligand: 0O2; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 4qrh.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1JXM 5GP 42.381
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