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Receptor
PDB id Resolution Class Description Source Keywords
2BNE 2.3 Å EC: 2.7.4.4 THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH UMP ESCHERICHIA COLI TRANSFERASE NUCLEOSIDE MONOPHOSPHATE KINASE PYRIMIDINE BIOSYNTHESIS
Ref.: STRUCTURE OF ESCHERICHIA COLI UMP KINASE DIFFERS FROM THAT OF OTHER NUCLEOSIDE MONOPHOSPHATE KINASES AND SHEDS NEW LIGHT ON ENZYME REGULATION. J.BIOL.CHEM. V. 280 25533 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1243;
A:1244;
A:1245;
A:1246;
B:1243;
B:1244;
B:1245;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
U5P A:1242;
B:1242;
Valid;
Valid;
none;
none;
submit data
324.181 C9 H13 N2 O9 P C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2BNE 2.3 Å EC: 2.7.4.4 THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH UMP ESCHERICHIA COLI TRANSFERASE NUCLEOSIDE MONOPHOSPHATE KINASE PYRIMIDINE BIOSYNTHESIS
Ref.: STRUCTURE OF ESCHERICHIA COLI UMP KINASE DIFFERS FROM THAT OF OTHER NUCLEOSIDE MONOPHOSPHATE KINASES AND SHEDS NEW LIGHT ON ENZYME REGULATION. J.BIOL.CHEM. V. 280 25533 2005
Members (1)
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....
70% Homology Family (1)
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....
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: U5P; Similar ligands found: 121
No: Ligand ECFP6 Tc MDL keys Tc
1 U 1 1
2 U5P 1 1
3 44P 0.790323 0.941176
4 UDP 0.78125 0.984615
5 UTP 0.746269 0.984615
6 2KH 0.735294 0.955224
7 UDP UDP 0.727273 0.953846
8 UPU 0.694444 0.954545
9 UNP 0.690141 0.955224
10 660 0.662338 0.913043
11 URM 0.662338 0.913043
12 URI 0.661017 0.848485
13 GUD 0.641026 0.926471
14 UFM 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GDU 0.641026 0.926471
17 UPF 0.6375 0.875
18 U2F 0.6375 0.875
19 Y6W 0.632911 0.875
20 UDH 0.628205 0.851351
21 UPP 0.628205 0.926471
22 UFG 0.617284 0.875
23 CJB 0.603175 0.80597
24 UDX 0.597561 0.926471
25 UAD 0.597561 0.926471
26 3UC 0.588235 0.875
27 U U 0.585366 0.969697
28 UGB 0.583333 0.940298
29 USQ 0.583333 0.807692
30 UGA 0.583333 0.940298
31 5FU 0.57971 0.927536
32 G3N 0.576471 0.9
33 UA3 0.573529 0.953846
34 U3P 0.573529 0.953846
35 CAR 0.571429 0.941176
36 C 0.571429 0.941176
37 C5P 0.571429 0.941176
38 UDM 0.568182 0.9
39 5BU 0.56338 0.927536
40 U4S 0.557143 0.763889
41 UD1 0.555556 0.913043
42 UD2 0.555556 0.913043
43 CSQ 0.550562 0.863014
44 CSV 0.550562 0.863014
45 U2S 0.541667 0.777778
46 U3S 0.541667 0.763889
47 CNU 0.540541 0.941176
48 S5P 0.535211 0.901408
49 16B 0.534247 0.901408
50 U2P 0.528571 0.939394
51 DU 0.527778 0.911765
52 UMP 0.527778 0.911765
53 HP7 0.526882 0.926471
54 UD7 0.526882 0.913043
55 MJZ 0.521277 0.9
56 UP6 0.521127 0.884058
57 12V 0.515789 0.887324
58 F5G 0.515789 0.913043
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 F5P 0.515789 0.9
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 NUP 0.506849 0.927536
66 U6M 0.506849 0.969697
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 4TC 0.5 0.818182
71 JW5 0.5 0.955224
72 EEB 0.49505 0.887324
73 A U 0.49505 0.815789
74 EPU 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 OMP 0.480519 0.969697
78 6AU 0.480519 0.969697
79 6CN 0.480519 0.941176
80 TKW 0.48 0.927536
81 UMF 0.479452 0.869565
82 UUA 0.477612 0.757576
83 U U U U 0.476744 0.954545
84 BMQ 0.472222 0.939394
85 PUP 0.47191 0.926471
86 G U 0.471154 0.797468
87 5HM 0.467532 0.888889
88 O7E 0.463415 0.941176
89 ICR 0.460526 0.830986
90 UMA 0.458716 0.9
91 O7M 0.45679 0.941176
92 UC5 0.455696 0.885714
93 UTP U U U 0.454545 0.909091
94 CDP 0.45 0.927536
95 2TU 0.449275 0.760563
96 FNU 0.441558 0.876712
97 2QR 0.439655 0.810127
98 DUD 0.4375 0.898551
99 N3E 0.4375 0.743243
100 2OM 0.435897 0.925373
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 U22 0.434783 0.777778
104 DUT 0.433735 0.898551
105 HF4 0.433735 0.927536
106 CTP 0.433735 0.927536
107 8OP 0.428571 0.849315
108 8GM 0.421687 0.853333
109 5GW 0.420455 0.927536
110 U A A U 0.418803 0.853333
111 4RA 0.414634 0.842105
112 DUP 0.411765 0.873239
113 DUN 0.409639 0.873239
114 UD0 0.408 0.831169
115 UVC 0.407895 0.842857
116 UM3 0.407895 0.897059
117 C5G 0.404255 0.875
118 UPA 0.401869 0.828947
119 A U C C 0.401639 0.794872
120 UAG 0.4 0.851351
121 A G U 0.4 0.7875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2BNE; Ligand: U5P; Similar sites found with APoc: 155
This union binding pocket(no: 1) in the query (biounit: 2bne.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1HBK MYR None
3 6FHQ DE5 None
4 3CTR MGP None
5 3WUR O4B 1.16959
6 4D06 NAR 1.65975
7 3K7S R52 1.67598
8 4WOP CTP 1.77778
9 3THR C2F 2.07469
10 1QXA GLY GLY GLY 2.12766
11 1UPF URF 2.23214
12 2NV2 GLN 2.45098
13 3PUN FUC GAL NDG FUC 2.48963
14 2WPF WPF 2.48963
15 2WPF FAD 2.48963
16 5U97 PIT 2.48963
17 2F5Z FAD 2.48963
18 5OLK DTP 2.48963
19 2ZX2 RAM 2.5641
20 3CTL S6P 2.5974
21 5IXB LGA 2.77778
22 3O01 DXC 2.90456
23 4LHD GLY 2.90456
24 2I4O ATP 2.90456
25 5IM3 DTP 2.90456
26 2Q7V FAD 2.90456
27 1TL2 NDG 2.9661
28 4IV9 FAD 3.3195
29 3AQT RCO 3.3195
30 2JB2 FAD 3.3195
31 2JB2 PHE 3.3195
32 1J78 OLA 3.3195
33 2CXG GLC GLC 3.3195
34 3VOZ 04A 3.3195
35 4Z24 FAD 3.3195
36 2JDU MFU 3.47826
37 6FOG OXL 3.57143
38 1O5O U5P 3.61991
39 5W7B MYR 3.73444
40 4UCI ADN 3.73444
41 3KCC CMP 3.73444
42 4GK9 MAN BMA MAN MAN MAN 3.73444
43 5LUB 3Y7 3.73444
44 1RTF BEN 3.73444
45 5HWK BEZ 3.75
46 3KP6 SAL 3.97351
47 5NGZ 2BG 4.06091
48 3K3G MMU 4.14938
49 2D09 FLV 4.14938
50 1T9D P22 4.14938
51 3OZG SSI 4.14938
52 5C2N NAG 4.16667
53 4P86 5GP 4.37158
54 3R51 MMA 4.375
55 4U8P UDP 4.56432
56 4YKG NAD 4.56432
57 5ZI9 FLC 4.56432
58 3P4X ADP 4.56432
59 4LFL TG6 4.65116
60 2GJ8 ALF GDP 4.65116
61 2DBX GLU 4.73684
62 5AHW CMP 4.7619
63 2GUC MAN 4.91803
64 2HYQ MAN MAN 4.91803
65 2GUD MAN 4.91803
66 2NUO BGC 4.91803
67 2NU5 NAG 4.91803
68 2GUD BMA 4.91803
69 2HYR BGC GLC 4.91803
70 3B9Q MLI 4.97925
71 1I0B PEL 4.97925
72 3MBI HSX 4.97925
73 3KIH GDL 5.15464
74 4JF5 FLC 5.39419
75 6MVU K4V 5.39419
76 3F5A SIA GAL NAG 5.39419
77 4YDD MD1 5.39419
78 4YDD MGD 5.39419
79 1MID LAP 5.49451
80 4P83 U5P 5.49451
81 1XTT U5P 5.55556
82 2GBB CIT 5.76923
83 4QYS PLR 5.80913
84 4UP3 FAD 5.80913
85 1FDJ 13P 5.80913
86 4OGQ UMQ 5.80913
87 3KO0 TFP 5.94059
88 4UXU MLK 5.9633
89 5GVR LMR 5.98291
90 4RW3 PLM 6.22407
91 4JLS 3ZE 6.57895
92 1IK4 PGH 6.57895
93 1BGV GLU 7.05394
94 5YBL AKG 7.05394
95 4Q86 AMP 7.05394
96 2BOI MFU 7.07965
97 2JBH 5GP 7.11111
98 3O5N BR0 7.14286
99 3HP8 SUC 7.27273
100 1ZED PNP 7.46888
101 1GPM AMP 7.46888
102 2A8X FAD 7.46888
103 4MOP 2H5 7.88382
104 3LN9 FLC 7.91367
105 2CJU PHX 8.26446
106 5WXU FLC 8.29876
107 3LL5 IP8 8.29876
108 4ISS TAR 8.29876
109 2YY8 MTA 8.45771
110 5UGW GSH 8.57143
111 6AR9 3L4 8.71369
112 5IFK HPA 8.71369
113 5H4S RAM 8.71369
114 1P4V GLY 8.71369
115 2UYQ SAM 9.12863
116 1NAA 6FA 9.12863
117 1NAA ABL 9.12863
118 1O8B ABF 9.13242
119 1T0S BML 9.30233
120 1Z0N BCD 9.375
121 1GRN AF3 9.42408
122 2NGR AF3 9.42408
123 2J5V RGP 9.54357
124 3RYC GTP 9.79021
125 3CF6 SP1 10.1796
126 4CR6 MAN 10.3321
127 4ARE FLC 10.3734
128 2YG3 FAD 10.3734
129 2BFR ADP 10.4167
130 3N7S 3N7 10.4348
131 1APZ ASP 10.4938
132 3GD8 GOL 10.7623
133 5FII PHE 10.7843
134 1GG6 APL 11.3402
135 2HQM FAD 11.6183
136 5LXT GDP 11.8881
137 1Y4Z PCI 12.8631
138 2QQD AG2 13.2075
139 1N13 AG2 13.4615
140 1M0S CIT 13.6986
141 2FAV APR 15.5556
142 1HE1 AF3 15.5556
143 3AB4 THR 15.7676
144 5LWY OLB 15.9664
145 2DT9 THR 16.1677
146 2BES RES 16.2791
147 2NLQ GLY 16.6667
148 3QFA FAD 19.8276
149 3K56 IS3 20.7469
150 5OSW DIU 22.4066
151 2RIF AMP 24.8227
152 5C9J DAO 25.2525
153 3RNM FAD 34.4828
154 1FQJ ALF 42.8571
155 2J4K U5P 46.4602
Pocket No.: 2; Query (leader) PDB : 2BNE; Ligand: U5P; 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: 2bne.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2BNE; Ligand: U5P; 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: 2bne.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2BNE; Ligand: U5P; Similar sites found with APoc: 23
This union binding pocket(no: 4) in the query (biounit: 2bne.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 6HT0 GQ8 None
2 4LNP VAL PRO PRO PRO ARG PRO PRO PRO PRO GLU None
3 2B9W FAD 1.65975
4 5D85 FLC 1.65975
5 3ESS 18N 2.17391
6 1V59 FAD 2.48963
7 6B74 BEN 2.90456
8 4FMS BDP 3.3195
9 4BQS ADP 3.40909
10 4Q0A 4OA 4.14938
11 5N6N SUC 4.16667
12 2HXW FLC 4.21941
13 3F8D FAD 4.56432
14 2VAR AMP 4.56432
15 2G50 ALA 5.39419
16 5T85 44G 5.52147
17 1BZL FAD 5.80913
18 2V7B BEZ 6.22407
19 5N26 CPT 7.14286
20 4M52 FAD 7.46888
21 2D3N GLC GLC GLC 9.95851
22 5YZC NAG 18.0851
23 3EHH ADP 18.8073
Pocket No.: 5; Query (leader) PDB : 2BNE; Ligand: U5P; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2bne.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2BNE; Ligand: U5P; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2bne.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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