Receptor
PDB id Resolution Class Description Source Keywords
4A7W 1.8 Å EC: 2.7.4.22 CRYSTAL STRUCTURE OF URIDYLATE KINASE FROM HELICOBACTER PYLORI HELICOBACTER PYLORI TRANSFERASE
Ref.: STRUCTURES OF HELICOBACTER PYLORI URIDYLATE KINASE: INTO RELEASE OF THE PRODUCT UDP ACTA CRYSTALLOGR.,SECT.D V. 68 773 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1242;
B:1242;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
GTP A:1241;
B:1241;
Valid;
Valid;
none;
none;
submit data
523.18 C10 H16 N5 O14 P3 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4A7W 1.8 Å EC: 2.7.4.22 CRYSTAL STRUCTURE OF URIDYLATE KINASE FROM HELICOBACTER PYLORI HELICOBACTER PYLORI TRANSFERASE
Ref.: STRUCTURES OF HELICOBACTER PYLORI URIDYLATE KINASE: INTO RELEASE OF THE PRODUCT UDP ACTA CRYSTALLOGR.,SECT.D V. 68 773 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4A7X - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 4A7W - GTP C10 H16 N5 O14 P3 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 2 families.
1 4A7X - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 4A7W - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2BNE - U5P C9 H13 N2 O9 P C1=CN(C(=O....
2 4A7X - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 4A7W - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GTP; Similar ligands found: 147
No: Ligand ECFP6 Tc MDL keys Tc
1 GTP 1 1
2 GP3 0.921053 0.973684
3 GDP 0.909091 1
4 GSP 0.853659 0.948718
5 GNH 0.82716 0.986667
6 G1R 0.819277 0.986667
7 GAV 0.811765 0.961039
8 GNP 0.809524 0.973684
9 GCP 0.797619 0.973684
10 5GP 0.797468 0.986486
11 G 0.797468 0.986486
12 GMV 0.764706 0.973684
13 G2R 0.764045 0.961039
14 G5P 0.755319 0.973684
15 GTG 0.752688 0.936709
16 G2P 0.747126 0.961039
17 G3A 0.744681 0.973684
18 GDD 0.741935 0.961039
19 GKE 0.741935 0.961039
20 GDC 0.741935 0.961039
21 0O2 0.736264 0.986486
22 GP2 0.729412 0.961039
23 6CK 0.726316 0.936709
24 Y9Z 0.723404 0.902439
25 GPG 0.717391 0.961039
26 GFB 0.715789 0.961039
27 GDR 0.715789 0.961039
28 GDP MG 0.712644 0.923077
29 GDP BEF 0.704545 0.9
30 GPD 0.704082 0.925
31 JB2 0.693878 0.961039
32 GKD 0.693878 0.961039
33 GCP G 0.692308 0.935065
34 GDX 0.686869 0.973684
35 ALF 5GP 0.685393 0.888889
36 GTP MG 0.681319 0.923077
37 BEF GDP 0.681319 0.888889
38 GH3 0.681319 0.973333
39 YGP 0.677083 0.901235
40 G3D 0.67033 0.986486
41 GDP AF3 0.659574 0.888889
42 GDP ALF 0.659574 0.888889
43 DGT 0.659341 0.923077
44 GMP 0.658228 0.88
45 G4P 0.655914 0.986486
46 JB3 0.653846 0.948718
47 NGD 0.647619 0.961039
48 CAG 0.642202 0.880952
49 2MD 0.62963 0.891566
50 G G 0.622449 0.935065
51 MGP 0.619565 0.961039
52 U2G 0.616822 0.936709
53 6G0 0.612903 0.961039
54 MGD 0.612613 0.891566
55 TPG 0.608696 0.840909
56 CG2 0.605505 0.936709
57 GDP 7MG 0.601942 0.911392
58 FEG 0.601852 0.879518
59 ZGP 0.59633 0.869048
60 MD1 0.591304 0.891566
61 PGD 0.591304 0.925
62 3GP 0.590909 0.946667
63 GPX 0.581633 0.946667
64 DGI 0.580645 0.923077
65 IDP 0.576087 0.972973
66 DBG 0.567797 0.948718
67 FE9 0.555556 0.776596
68 2GP 0.555556 0.96
69 G4M 0.547619 0.880952
70 BGO 0.544643 0.924051
71 I2C FE2 CMO CMO 0.538462 0.808989
72 ATP 0.537634 0.92
73 G1G 0.533898 0.925
74 AQP 0.531915 0.92
75 5FA 0.531915 0.92
76 G A A A 0.525862 0.923077
77 U A G G 0.521368 0.935065
78 01G 0.518868 0.902439
79 ITT 0.510638 0.868421
80 P2G 0.510638 0.883117
81 GGM 0.504274 0.901235
82 G1R G1R 0.504065 0.924051
83 DGP 0.5 0.910256
84 PGD O 0.5 0.850575
85 MGO 0.5 0.864198
86 P1G 0.5 0.871795
87 DG 0.5 0.910256
88 GTA 0.495495 0.936709
89 B4P 0.489362 0.894737
90 AP5 0.489362 0.894737
91 IMP 0.489362 0.959459
92 7DT 0.484536 0.906667
93 G G U 0.482143 0.935065
94 GPC 0.479339 0.879518
95 G C 0.478992 0.9
96 BA3 0.478723 0.894737
97 ADP 0.473684 0.92
98 G2Q 0.471698 0.961039
99 G7M 0.46875 0.948052
100 25L 0.458716 0.907895
101 A2D 0.457447 0.894737
102 RGT 0.45045 0.909091
103 AGS 0.45 0.873418
104 SAP 0.45 0.873418
105 SGP 0.44898 0.82716
106 U G A 0.448529 0.888889
107 A4P 0.445378 0.869048
108 G G G RPC 0.442623 0.875
109 ACQ 0.441176 0.896104
110 ANP 0.441176 0.896104
111 8GT 0.441176 0.875
112 APC G U 0.44 0.886076
113 G U34 0.438017 0.888889
114 6AD 0.436893 0.841463
115 G G G C 0.433071 0.9125
116 UP5 0.432203 0.873418
117 35G 0.431373 0.933333
118 C2E 0.431373 0.921053
119 PCG 0.431373 0.933333
120 A G C C 0.429688 0.911392
121 5GP 5GP 0.427184 0.883117
122 TAT 0.427184 0.884615
123 APR 0.425743 0.894737
124 AR6 0.425743 0.894737
125 AN2 0.424242 0.907895
126 7DD 0.424242 0.906667
127 DG DG 0.423423 0.865854
128 AD9 0.421569 0.896104
129 M33 0.42 0.883117
130 7D4 0.42 0.835443
131 UCG 0.419847 0.911392
132 H6Y 0.419048 0.946667
133 G C C C 0.416667 0.924051
134 ACP 0.415842 0.896104
135 T5A 0.414634 0.802326
136 MGQ 0.412844 0.935897
137 ADQ 0.412844 0.871795
138 A1R 0.412844 0.839506
139 MGT 0.411215 0.823529
140 A G U 0.410072 0.888889
141 93A 0.41 0.833333
142 A22 0.407407 0.907895
143 CA0 0.405941 0.896104
144 ATF 0.40566 0.884615
145 AGO 0.404762 0.888889
146 MGV 0.401786 0.890244
147 CGP 0.4 0.86747
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4A7W; Ligand: GTP; Similar sites found: 83
This union binding pocket(no: 1) in the query (biounit: 4a7w.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3MBG FAD 0.0134 0.42559 None
2 3O55 FAD 0.0219 0.41915 None
3 5X4Q 7Z6 0.01248 0.41752 None
4 3U5S FAD 0.01559 0.41499 None
5 3RV5 DXC 0.0103 0.40541 None
6 1JR8 FAD 0.03675 0.40208 None
7 1LRI CLR 0.03414 0.40128 None
8 5F1R 42O 0.03194 0.41248 1.26582
9 1PGP 6PG 0.003246 0.473 1.66667
10 4B5P ACO 0.0223 0.42334 2
11 3VHE 42Q 0.01539 0.42401 2.08333
12 4BVM VCA 0.01773 0.42329 2.25564
13 4BVM PLM 0.01661 0.42329 2.25564
14 2CB3 MLD 0.04027 0.40109 2.28571
15 1OQC FAD 0.01231 0.42339 2.4
16 3PFG TLO 0.003873 0.47374 2.5
17 4V3I ASP LEU THR ARG PRO 0.007054 0.41697 2.91667
18 4AG8 AXI 0.02841 0.4134 2.91667
19 4QJR PIZ 0.02957 0.41308 2.91667
20 1ZDT PEF 0.03261 0.41231 2.91667
21 4ASE AV9 0.02839 0.40442 2.91667
22 4ZOM 4Q3 0.01115 0.4401 3.11111
23 4DR9 BB2 0.02405 0.40585 3.125
24 4RHP PEF 0.02865 0.40006 3.40426
25 3GXO MQA 0.001135 0.46834 3.75
26 2OO8 RAJ 0.01346 0.42124 3.75
27 3JRX S1A 0.03268 0.4035 3.75
28 2CNT COA 0.04481 0.40272 3.75
29 2VWA PTY 0.01392 0.40515 3.9604
30 1BGQ RDC 0.02875 0.41725 4
31 1YC4 43P 0.02032 0.40724 4.16667
32 3D78 NBB 0.02651 0.41931 4.20168
33 5BVT PAM 0.01743 0.41947 4.47761
34 2IFB PLM 0.02954 0.41168 4.58015
35 1IF7 SBR 0.04398 0.43621 4.58333
36 5X80 SAL 0.02645 0.40909 4.58333
37 5JKG 6LF 0.04208 0.40346 4.58333
38 3QMK SGN IDS SGN IDS 0.04101 0.41691 4.6729
39 4RC8 STE 0.03918 0.40193 4.95496
40 3HLX PQQ 0.007325 0.44227 5
41 3FPF MTA 0.04804 0.41273 5
42 3FPF TNA 0.04804 0.41273 5
43 1YMT DR9 0.02411 0.42201 5.41667
44 1NQ7 ARL 0.01885 0.41156 5.41667
45 3K8L MT7 0.02627 0.40964 5.41667
46 2HJ3 FAD 0.01355 0.41699 5.6
47 3WBG 2AN 0.01582 0.41356 5.88235
48 5HZ9 5M8 0.01232 0.4257 5.92593
49 2VH6 GSV 0.02695 0.40844 5.97015
50 2IZ1 ATR 0.01719 0.42933 6.25
51 2OFV 242 0.02327 0.42355 6.25
52 2R40 20E 0.006909 0.44522 6.66667
53 5WX3 COA 0.01698 0.42587 7.08333
54 1N83 CLR 0.01401 0.42397 7.5
55 1QY8 RDI 0.02461 0.40605 7.5
56 5N8V KZZ 0.01299 0.41067 8.69565
57 4U0I 0LI 0.02034 0.41834 8.75
58 3GFZ FMN 0.02084 0.40573 8.75
59 4OMJ 2TX 0.03094 0.42044 9.16667
60 1OLM VTQ 0.02877 0.41546 9.16667
61 4XPL ACO 0.02337 0.40337 9.20245
62 4H6U ACO 0.02785 0.4036 9.5
63 1RJ9 GCP 0.04449 0.41074 9.53947
64 1GJW GLC 0.005621 0.41905 9.58333
65 2NNQ T4B 0.03314 0.42469 10
66 3RGA ILD 0.01987 0.42077 10.4167
67 2GVJ DGB 0.02527 0.40672 10.4167
68 5CFT 51G 0.0333 0.40155 10.8108
69 5CFT APC 0.0293 0.40155 10.8108
70 5U98 1KX 0.0467 0.42556 11.1111
71 1EE0 CAA 0.02541 0.42107 11.6667
72 5HZ5 65X 0.01385 0.43031 11.9403
73 1P72 ADP 0.0271 0.41833 13.3333
74 2QO4 CHD 0.02264 0.42649 14.2857
75 4LN7 1ZQ 0.01628 0.40978 14.5833
76 5APK 76E 0.02157 0.41975 15
77 5X8Q 82R 0.01026 0.43351 15.4167
78 5NTW 98N 0.01041 0.44392 15.8333
79 4AZP A9M 0.02385 0.41756 15.942
80 3UR0 SVR 0.04713 0.41394 17.0833
81 1YRX FMN 0.02637 0.40167 17.3554
82 2QM9 TDZ 0.02546 0.41482 17.5
83 5IJJ I6P 0.002078 0.44996 20.8333
Pocket No.: 2; Query (leader) PDB : 4A7W; Ligand: GTP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4a7w.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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