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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: 156
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 9GM 0.809524 0.973684
9 GNP 0.809524 0.973684
10 GCP 0.797619 0.973684
11 5GP 0.797468 0.986486
12 G 0.797468 0.986486
13 GMV 0.764706 0.973684
14 G2R 0.764045 0.961039
15 G5P 0.755319 0.973684
16 GTG 0.752688 0.936709
17 G2P 0.747126 0.961039
18 G3A 0.744681 0.973684
19 GDD 0.741935 0.961039
20 GDC 0.741935 0.961039
21 GKE 0.741935 0.961039
22 0O2 0.736264 0.986486
23 GP2 0.729412 0.961039
24 6CK 0.726316 0.936709
25 Y9Z 0.723404 0.902439
26 GPG 0.717391 0.961039
27 GFB 0.715789 0.961039
28 GDR 0.715789 0.961039
29 GPD 0.704082 0.925
30 GKD 0.693878 0.961039
31 JB2 0.693878 0.961039
32 GDX 0.686869 0.973684
33 ALF 5GP 0.685393 0.888889
34 GH3 0.681319 0.973333
35 YGP 0.677083 0.901235
36 G3D 0.67033 0.986486
37 GDP AF3 0.659574 0.888889
38 ALF GDP 0.659574 0.888889
39 GDP ALF 0.659574 0.888889
40 DGT 0.659341 0.923077
41 GMP 0.658228 0.88
42 G4P 0.655914 0.986486
43 JB3 0.653846 0.948718
44 NGD 0.647619 0.961039
45 CAG 0.642202 0.880952
46 2MD 0.62963 0.891566
47 MGP 0.619565 0.961039
48 U2G 0.616822 0.936709
49 6G0 0.612903 0.961039
50 MGD 0.612613 0.891566
51 TPG 0.608696 0.840909
52 CG2 0.605505 0.936709
53 GDP 7MG 0.601942 0.911392
54 FEG 0.601852 0.879518
55 G G 0.598039 0.948052
56 ZGP 0.59633 0.869048
57 PGD 0.591304 0.925
58 MD1 0.591304 0.891566
59 3GP 0.590909 0.946667
60 GPX 0.581633 0.946667
61 DGI 0.580645 0.923077
62 IDP 0.576087 0.972973
63 DBG 0.567797 0.948718
64 2GP 0.555556 0.96
65 FE9 0.555556 0.776596
66 G4M 0.547619 0.880952
67 BGO 0.544643 0.924051
68 GCP G 0.543689 0.921053
69 ATP 0.537634 0.92
70 HEJ 0.537634 0.92
71 G1G 0.533898 0.925
72 AQP 0.531915 0.92
73 5FA 0.531915 0.92
74 A G 0.525862 0.935065
75 G A A A 0.525862 0.923077
76 U A G G 0.521368 0.935065
77 HFD 0.520833 0.873418
78 R5I 0.520408 0.946667
79 R7I 0.520408 0.946667
80 01G 0.518868 0.902439
81 P2G 0.510638 0.883117
82 ITT 0.510638 0.868421
83 AKW 0.504348 0.890244
84 GGM 0.504274 0.901235
85 G1R G1R 0.504065 0.924051
86 DGP 0.5 0.910256
87 PGD O 0.5 0.850575
88 MGO 0.5 0.864198
89 DG 0.5 0.910256
90 P1G 0.5 0.871795
91 GTA 0.495495 0.936709
92 PRT 0.490741 0.959459
93 B4P 0.489362 0.894737
94 AP5 0.489362 0.894737
95 IMP 0.489362 0.959459
96 G U 0.487179 0.9
97 7DT 0.484536 0.906667
98 GPC 0.479339 0.879518
99 G C 0.478992 0.9
100 BA3 0.478723 0.894737
101 ADP 0.473684 0.92
102 G2Q 0.471698 0.961039
103 6YZ 0.470588 0.896104
104 G7M 0.46875 0.948052
105 C1Z 0.462963 0.986486
106 25L 0.458716 0.907895
107 A2D 0.457447 0.894737
108 RGT 0.45045 0.909091
109 AGS 0.45 0.873418
110 SAP 0.45 0.873418
111 SGP 0.44898 0.82716
112 A4P 0.445378 0.869048
113 G G G RPC 0.442623 0.875
114 ANP 0.441176 0.896104
115 ACQ 0.441176 0.896104
116 8GT 0.441176 0.875
117 APC G U 0.44 0.886076
118 AT4 0.438776 0.884615
119 G U34 0.438017 0.888889
120 6AD 0.436893 0.841463
121 G G G C 0.433071 0.9125
122 UP5 0.432203 0.873418
123 PCG 0.431373 0.933333
124 C2E 0.431373 0.921053
125 35G 0.431373 0.933333
126 A G C C 0.429688 0.911392
127 T99 0.427184 0.884615
128 5GP 5GP 0.427184 0.883117
129 TAT 0.427184 0.884615
130 AR6 0.425743 0.894737
131 APR 0.425743 0.894737
132 7DD 0.424242 0.906667
133 AN2 0.424242 0.907895
134 DG DG 0.423423 0.865854
135 AD9 0.421569 0.896104
136 M33 0.42 0.883117
137 7D4 0.42 0.835443
138 UCG 0.419847 0.911392
139 HDV 0.419048 0.825
140 H6Y 0.419048 0.946667
141 G C C C 0.416667 0.924051
142 ACP 0.415842 0.896104
143 T5A 0.414634 0.802326
144 A1R 0.412844 0.839506
145 ADQ 0.412844 0.871795
146 MGQ 0.412844 0.935897
147 A3R 0.412844 0.839506
148 MGT 0.411215 0.823529
149 A G U 0.410072 0.888889
150 93A 0.41 0.833333
151 A22 0.407407 0.907895
152 CA0 0.405941 0.896104
153 ATF 0.40566 0.884615
154 AGO 0.404762 0.888889
155 MGV 0.401786 0.890244
156 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 with APoc: 145
This union binding pocket(no: 1) in the query (biounit: 4a7w.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 5N1X 8HH None
2 3MBG FAD None
3 3O55 FAD None
4 5X4Q 7Z6 None
5 1UO5 PIH None
6 3RV5 DXC None
7 1JR8 FAD None
8 1LRI CLR None
9 3FXU TSU 1.25
10 5F1R 42O 1.26582
11 4ZAL 4LR 1.43541
12 4ZAL FNR 1.43541
13 1PGP 6PG 1.66667
14 4B5P ACO 2
15 2GWH PCI 2.08333
16 3VHE 42Q 2.08333
17 4BVM VCA 2.25564
18 4BVM PLM 2.25564
19 2CB3 MLD 2.28571
20 1OQC FAD 2.4
21 3PFG SAM 2.5
22 3PFG TLO 2.5
23 4TWP AXI 2.5
24 3GWL FAD 2.83019
25 5YGE GLU 2.87356
26 5W8Q BU4 2.91667
27 1ZDT PEF 2.91667
28 6C3C EJ1 2.91667
29 4AG8 AXI 2.91667
30 4QJR PIZ 2.91667
31 5GVL GI8 2.91667
32 5GVL PLG 2.91667
33 4ASE AV9 2.91667
34 4V3I ASP LEU THR ARG PRO 2.91667
35 6FS8 E4Z 2.92683
36 3WR7 COA 2.94118
37 5W7U GY8 3.04569
38 4DR9 BB2 3.125
39 1WS1 BB2 3.20513
40 5NM7 GLY 3.33333
41 5BYK OAQ 3.33333
42 5BYK A3P 3.33333
43 5LX9 OLB 3.33333
44 4RHP PEF 3.40426
45 4JE7 BB2 3.5533
46 1JGS SAL 3.62319
47 2OO8 RAJ 3.75
48 4YUS FMN 3.75
49 3GXO MQA 3.75
50 1RPN NDP 3.75
51 3JRX S1A 3.75
52 2CNT COA 3.75
53 2VWA PTY 3.9604
54 1BGQ RDC 4
55 4RW3 TDA 4.16667
56 4RW3 PLM 4.16667
57 3E70 GDP 4.16667
58 1YC4 43P 4.16667
59 5B47 TPP 4.16667
60 5B47 PYR 4.16667
61 3D78 NBB 4.20168
62 4QC6 30N 4.46927
63 5BVT PAM 4.47761
64 5UC4 83S 4.54545
65 2IFB PLM 4.58015
66 6C9B EGV 4.58333
67 6C92 EQJ 4.58333
68 6C8T EQJ 4.58333
69 3W5N RAM 4.58333
70 5NEA 8V8 4.58333
71 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 4.58333
72 6C92 EGV 4.58333
73 5X80 SAL 4.58333
74 5JKG 6LF 4.58333
75 3NB0 G6P 4.58333
76 3QMK SGN IDS SGN IDS 4.6729
77 4XOQ F42 4.83092
78 4RC8 STE 4.95496
79 3HLX PQQ 5
80 3FPF MTA 5
81 3FPF TNA 5
82 4R57 ACO 5.11364
83 1YMT DR9 5.41667
84 1NQ7 ARL 5.41667
85 2HJ3 FAD 5.6
86 3WBG 2AN 5.88235
87 5HZ9 5M8 5.92593
88 2VH6 GSV 5.97015
89 4RHE FMN 6.2201
90 1N1G BCP 6.25
91 2IZ1 ATR 6.25
92 6EQ8 BQZ 6.25
93 2OBD PCW 6.25
94 2OFV 242 6.25
95 2R40 20E 6.66667
96 1ZED PNP 6.66667
97 1FP2 HMO 6.66667
98 1RKX NAD 6.66667
99 5WX3 COA 7.08333
100 4KVL PLM 7.08333
101 1N83 CLR 7.5
102 6D28 NEC 7.5
103 2GFD RDA 7.62712
104 2D5X L35 8.21918
105 5N26 CPT 8.24176
106 6MVU K4V 8.33333
107 5N8V KZZ 8.69565
108 5XWV 8H6 8.75
109 4U0I 0LI 8.75
110 4H03 LAR 8.75
111 3GFZ FMN 8.75
112 3WYJ H78 9.16667
113 4OMJ 2TX 9.16667
114 1OLM VTQ 9.16667
115 4XPL ACO 9.20245
116 4H6U ACO 9.5
117 1RJ9 GCP 9.53947
118 1GJW GLC 9.58333
119 2NNQ T4B 10
120 5OCA 9QZ 10
121 3RGA ILD 10.4167
122 2GVJ DGB 10.4167
123 6EVN PRO PRO GLY PRO ALA GLY PRO PRO GLY 10.7843
124 5CFT APC 10.8108
125 5CFT 51G 10.8108
126 5U98 1KX 11.1111
127 1NU4 MLA 11.3402
128 1EE0 CAA 11.6667
129 5HZ5 65X 11.9403
130 1T0S BML 12.9167
131 1P72 ADP 13.3333
132 2QO4 CHD 14.2857
133 5APK 76E 15
134 5X8Q 82R 15.4167
135 5NTW 98N 15.8333
136 4AZP A9M 15.942
137 5Z84 CHD 17.0213
138 5ZCO CHD 17.0213
139 5Z84 TGL 17.0213
140 5ZCO TGL 17.0213
141 3UR0 SVR 17.0833
142 1YRX FMN 17.3554
143 2QM9 TDZ 17.5
144 2AIB ERG 20.4082
145 5IJJ I6P 20.8333
Pocket No.: 2; Query (leader) PDB : 4A7W; Ligand: GTP; Similar sites found with APoc: 9
This union binding pocket(no: 2) in the query (biounit: 4a7w.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 3ANP DCC None
2 2YFB SIN 2.08333
3 3KJS DQ1 2.91667
4 4X60 3XV 3.75
5 1D6H COA 4.58333
6 1J3I NDP 6.66667
7 4C1K PEP 6.66667
8 4M4Q 21A 7.88382
9 5T67 SAH 11.25
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