Receptor
PDB id Resolution Class Description Source Keywords
5XKT 1.8 Å EC: 7.-.-.- KLEBSIELLA PNEUMONIAE UREG IN COMPLEX WITH GMPPNP AND NICKEL KLEBSIELLA PNEUMONIAE SUBSP. RHINOSCLESB3432 SIMIBI CLASS GTPASE HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO HOW GTP-DEPENDENT CONFORMA CHANGES IN A METALLOCHAPERONE UREG FACILITATE UREAS MATURATION. PROC. NATL. ACAD. SCI. V. 114 10890 2017 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GNP B:500;
A:301;
Valid;
Valid;
none;
none;
submit data
522.196 C10 H17 N6 O13 P3 c1nc2...
NI A:303;
B:501;
A:302;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
58.693 Ni [Ni+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5XKT 1.8 Å EC: 7.-.-.- KLEBSIELLA PNEUMONIAE UREG IN COMPLEX WITH GMPPNP AND NICKEL KLEBSIELLA PNEUMONIAE SUBSP. RHINOSCLESB3432 SIMIBI CLASS GTPASE HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO HOW GTP-DEPENDENT CONFORMA CHANGES IN A METALLOCHAPERONE UREG FACILITATE UREAS MATURATION. PROC. NATL. ACAD. SCI. V. 114 10890 2017 U.S.A.
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 5XKT - GNP C10 H17 N6 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 250 families.
1 5XKT - GNP C10 H17 N6 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 204 families.
1 5XKT - GNP C10 H17 N6 O13 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GNP; Similar ligands found: 132
No: Ligand ECFP6 Tc MDL keys Tc
1 GNP 1 1
2 9GM 1 1
3 GDP 0.839506 0.973684
4 GP3 0.82716 0.948718
5 GTP 0.809524 0.973684
6 GNH 0.807229 0.986842
7 G1R 0.77907 0.961039
8 GCP 0.77907 0.948718
9 GSP 0.770115 0.925
10 5GP 0.756098 0.960526
11 G 0.756098 0.960526
12 G2R 0.747253 0.936709
13 GMV 0.747126 0.948718
14 GAV 0.714286 0.936709
15 GP2 0.712644 0.936709
16 G2P 0.711111 0.936709
17 Y9Z 0.708333 0.880952
18 GDC 0.690722 0.936709
19 GDD 0.690722 0.936709
20 GKE 0.690722 0.936709
21 G5P 0.686869 0.948718
22 GPG 0.684211 0.936709
23 GTG 0.683673 0.91358
24 GDR 0.683673 0.936709
25 GFB 0.683673 0.936709
26 JB2 0.68 0.936709
27 GKD 0.68 0.936709
28 6CK 0.676768 0.91358
29 G3A 0.676768 0.948718
30 GDX 0.673267 0.948718
31 ALF 5GP 0.67033 0.86747
32 YGP 0.663265 0.879518
33 GPD 0.656863 0.902439
34 ALF GDP 0.645833 0.86747
35 GDP AF3 0.645833 0.86747
36 GDP ALF 0.645833 0.86747
37 JB3 0.641509 0.925
38 DBG 0.640351 0.974359
39 G3D 0.638298 0.960526
40 G4P 0.625 0.960526
41 GMP 0.621951 0.857143
42 NGD 0.62037 0.936709
43 GGM 0.618182 0.925926
44 0O2 0.616162 0.960526
45 2MD 0.603604 0.870588
46 CAG 0.60177 0.904762
47 U2G 0.590909 0.91358
48 FEG 0.590909 0.858824
49 GDP 7MG 0.590476 0.888889
50 MGD 0.587719 0.870588
51 G G 0.586538 0.924051
52 ZGP 0.585586 0.848837
53 CG2 0.580357 0.91358
54 ANP 0.568421 0.922078
55 PGD 0.567797 0.902439
56 MD1 0.567797 0.870588
57 3GP 0.56044 0.922078
58 TPG 0.558333 0.822222
59 GH3 0.55 0.948052
60 FE9 0.546219 0.778947
61 GPX 0.539216 0.922078
62 G4M 0.539062 0.860465
63 DGI 0.536082 0.9
64 BGO 0.535088 0.901235
65 IDP 0.53125 0.947368
66 DGT 0.53 0.9
67 2GP 0.526882 0.935065
68 G1R G1R 0.520325 0.901235
69 GCP G 0.518868 0.897436
70 A G 0.516949 0.911392
71 U A G G 0.512605 0.911392
72 G A A A 0.504202 0.9
73 AGO 0.504202 0.91358
74 P2G 0.5 0.860759
75 G1G 0.5 0.902439
76 R7I 0.49505 0.922078
77 MGP 0.49505 0.936709
78 R5I 0.49505 0.922078
79 PGD O 0.492063 0.831461
80 6G0 0.490196 0.936709
81 P1G 0.489796 0.85
82 AKW 0.483051 0.869048
83 DG 0.474227 0.8875
84 DGP 0.474227 0.8875
85 G U 0.466667 0.878049
86 IMP 0.463918 0.934211
87 G2Q 0.462963 0.936709
88 GPC 0.459677 0.858824
89 G C 0.459016 0.878049
90 GTA 0.448276 0.91358
91 G7M 0.444444 0.924051
92 MAP 0.439252 0.898734
93 G G G RPC 0.435484 0.853659
94 B4P 0.434343 0.871795
95 AP5 0.434343 0.871795
96 ADP 0.434343 0.896104
97 A2D 0.43299 0.871795
98 AT4 0.43 0.8625
99 G G G C 0.426357 0.890244
100 AU1 0.425743 0.922078
101 SGP 0.425743 0.807229
102 BA3 0.424242 0.871795
103 A G C C 0.423077 0.888889
104 35G 0.423077 0.909091
105 PCG 0.423077 0.909091
106 C2E 0.423077 0.897436
107 APC G U 0.421875 0.864198
108 HEJ 0.421569 0.896104
109 ATP 0.421569 0.896104
110 ACQ 0.419048 0.873418
111 5GP 5GP 0.419048 0.860759
112 5FA 0.417476 0.896104
113 AQP 0.417476 0.896104
114 01G 0.417391 0.880952
115 AN2 0.415842 0.909091
116 UNP 0.415842 0.810127
117 6AD 0.415094 0.821429
118 M33 0.411765 0.860759
119 ITT 0.411765 0.846154
120 G C C C 0.410448 0.901235
121 HFD 0.409524 0.851852
122 G U34 0.408 0.86747
123 ACP 0.407767 0.873418
124 6YZ 0.407407 0.873418
125 AR6 0.403846 0.871795
126 APR 0.403846 0.871795
127 DG DG 0.403509 0.845238
128 A4P 0.403226 0.848837
129 UCG 0.402985 0.888889
130 SAP 0.4 0.851852
131 AGS 0.4 0.851852
132 AD9 0.4 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5XKT; Ligand: GNP; Similar sites found with APoc: 31
This union binding pocket(no: 1) in the query (biounit: 5xkt.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 3N5C GDP 1.23457
2 1SKQ GDP 1.5
3 3AQ4 GDP 2.71739
4 1KK1 GNP 3
5 5W76 GDP 3
6 3Q72 GNP 3.01205
7 2RCN GDP 3.5
8 2CJW GDP 3.64583
9 4B47 GDP 4
10 4DKX GDP 4
11 2HT6 GDP 4.02299
12 3WYA GDP 4.5
13 3WY9 GDP 4.5
14 4P3Y GDP 5
15 3U6B GDP 5
16 1YZG GDP 5.58659
17 2WJG GDP 5.85106
18 5O74 GDP 6.11111
19 3MD0 GDP 7.04225
20 3CNL GNP 7.5
21 2WIC GNP 8
22 1RE0 GDP 8.5
23 4J0Q GDP 9
24 1ZJ6 G3D 9.09091
25 3T1O GDP 10
26 5YT0 GDP 10
27 5CK5 GDP 10.7595
28 1MKY GDP 11.5
29 2QN6 GDP 19.3548
30 1YRB GDP 20
31 1S8F GDP 27.1186
Pocket No.: 2; Query (leader) PDB : 5XKT; Ligand: GNP; 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: 5xkt.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
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