Receptor
PDB id Resolution Class Description Source Keywords
2J4K 2.2 Å EC: 2.7.4.22 CRYSTAL STRUCTURE OF URIDYLATE KINASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH UMP TO 2.2 ANGSTROM R ESOLUTION SULFOLOBUS SOLFATARICUS ASPARTOKINASE FAMILY PYRIMIDINE BIOSYNTHESIS KINASE UMP KINASE TRANSFERASE NUCLEOSIDE MONOPHOSPHATE KINASE PYRIMIDINE NUCLEOTIDE SYNTHESIS
Ref.: STRUCTURAL AND ENZYMATIC INVESTIGATION OF THE SULFOLOBUS SOLFATARICUS URIDYLATE KINASE SHOWS COMPETITIVE UTP INHIBITION AND THE LACK OF GTP STIMULATION BIOCHEMISTRY V. 46 2745 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CD A:228;
A:229;
A:230;
B:228;
B:229;
B:230;
B:231;
B:232;
B:233;
B:234;
C:228;
C:229;
C:231;
D:228;
E:228;
E:229;
F:228;
F:229;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
112.411 Cd [Cd+2...
MG A:231;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
U5P A:227;
B:227;
C:227;
D:227;
E:227;
F:227;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 14 uM
324.181 C9 H13 N2 O9 P C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2J4K 2.2 Å EC: 2.7.4.22 CRYSTAL STRUCTURE OF URIDYLATE KINASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH UMP TO 2.2 ANGSTROM R ESOLUTION SULFOLOBUS SOLFATARICUS ASPARTOKINASE FAMILY PYRIMIDINE BIOSYNTHESIS KINASE UMP KINASE TRANSFERASE NUCLEOSIDE MONOPHOSPHATE KINASE PYRIMIDINE NUCLEOTIDE SYNTHESIS
Ref.: STRUCTURAL AND ENZYMATIC INVESTIGATION OF THE SULFOLOBUS SOLFATARICUS URIDYLATE KINASE SHOWS COMPETITIVE UTP INHIBITION AND THE LACK OF GTP STIMULATION BIOCHEMISTRY V. 46 2745 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2J4J - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
2 2J4K Kd = 14 uM U5P C9 H13 N2 O9 P C1=CN(C(=O....
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 2J4J - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
2 2J4K Kd = 14 uM U5P C9 H13 N2 O9 P C1=CN(C(=O....
50% 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 2J4J - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
2 2J4K Kd = 14 uM U5P C9 H13 N2 O9 P C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: U5P; Similar ligands found: 120
No: Ligand ECFP6 Tc MDL keys Tc
1 U5P 1 1
2 44P 0.790323 0.941176
3 UDP 0.78125 0.984615
4 UTP 0.746269 0.984615
5 2KH 0.735294 0.955224
6 UDP UDP 0.727273 0.953846
7 UPU 0.694444 0.954545
8 UNP 0.690141 0.955224
9 URM 0.662338 0.913043
10 660 0.662338 0.913043
11 URI 0.661017 0.848485
12 U 0.661017 0.848485
13 UFM 0.641026 0.926471
14 GDU 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GUD 0.641026 0.926471
17 U2F 0.6375 0.875
18 UPF 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 UDP GAL 0.597561 0.898551
27 3UC 0.588235 0.875
28 U U 0.585366 0.969697
29 UGB 0.583333 0.940298
30 USQ 0.583333 0.807692
31 UGA 0.583333 0.940298
32 5FU 0.57971 0.927536
33 G3N 0.576471 0.9
34 U3P 0.573529 0.953846
35 UA3 0.573529 0.953846
36 C 0.571429 0.941176
37 CH 0.571429 0.926471
38 CAR 0.571429 0.941176
39 C5P 0.571429 0.941176
40 UDM 0.568182 0.9
41 5BU 0.56338 0.927536
42 U4S 0.557143 0.763889
43 UD1 0.555556 0.913043
44 UD2 0.555556 0.913043
45 CSQ 0.550562 0.863014
46 CSV 0.550562 0.863014
47 U3S 0.541667 0.763889
48 U2S 0.541667 0.777778
49 CNU 0.540541 0.941176
50 S5P 0.535211 0.901408
51 16B 0.534247 0.901408
52 U2P 0.528571 0.939394
53 DU 0.527778 0.911765
54 UMP 0.527778 0.911765
55 HP7 0.526882 0.926471
56 UD7 0.526882 0.913043
57 MJZ 0.521277 0.9
58 UP6 0.521127 0.884058
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 12V 0.515789 0.887324
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 U6M 0.506849 0.969697
66 NUP 0.506849 0.927536
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 JW5 0.5 0.955224
71 4TC 0.5 0.818182
72 EPU 0.49505 0.887324
73 A U 0.49505 0.815789
74 EEB 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 6AU 0.480519 0.969697
78 OMP 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 5HM 0.467532 0.888889
87 O7E 0.463415 0.941176
88 ICR 0.460526 0.830986
89 UMA 0.458716 0.9
90 O7M 0.45679 0.941176
91 UC5 0.455696 0.885714
92 UTP U U U 0.454545 0.909091
93 CDP 0.45 0.927536
94 2TU 0.449275 0.760563
95 FNU 0.441558 0.876712
96 2QR 0.439655 0.810127
97 N3E 0.4375 0.743243
98 DUD 0.4375 0.898551
99 2OM 0.435897 0.925373
100 U22 0.434783 0.777778
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 DUT 0.433735 0.898551
104 CTP 0.433735 0.927536
105 8OP 0.428571 0.849315
106 8GM 0.421687 0.853333
107 5GW 0.420455 0.927536
108 U A A U 0.418803 0.853333
109 4RA 0.414634 0.842105
110 DUP 0.411765 0.873239
111 DUN 0.409639 0.873239
112 CDP MG 0.409639 0.861111
113 UD0 0.408 0.831169
114 UVC 0.407895 0.842857
115 UM3 0.407895 0.897059
116 C5G 0.404255 0.875
117 UPA 0.401869 0.828947
118 A U C C 0.401639 0.794872
119 A G U 0.4 0.7875
120 UAG 0.4 0.851351
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2J4K; Ligand: U5P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2j4k.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2J4K; Ligand: U5P; Similar sites found: 17
This union binding pocket(no: 2) in the query (biounit: 2j4k.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2RC8 DSN 0.02521 0.42389 2.21239
2 2DTJ THR 0.02921 0.40991 2.80899
3 2EUG URA 0.004459 0.47027 3.09735
4 3B9Q MLI 0.03148 0.43751 3.53982
5 1GS5 NLG 0.0001189 0.4366 3.53982
6 2QHV OC9 0.04042 0.40613 5.75221
7 1E19 ADP 0.002481 0.44758 7.07965
8 3RV5 DXC 0.04843 0.41259 7.86517
9 5H9I XAN 0.01335 0.43961 7.9646
10 3LL5 ADP 0.000000298 0.52872 9.29204
11 3LL5 IPE 0.000000174 0.52817 9.29204
12 3LL5 ATP 0.000002756 0.43494 9.29204
13 2IU8 PLM 0.006045 0.41927 11.0619
14 4F4S EFO 0.01846 0.42863 13.1579
15 3QUR FM4 0.000001513 0.49257 25.2212
16 2BNF UTP 0.0000001733 0.48891 43.8053
17 2BNE U5P 0.00000111 0.44416 46.4602
Pocket No.: 3; Query (leader) PDB : 2J4K; Ligand: U5P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2j4k.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2J4K; Ligand: U5P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2j4k.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2J4K; Ligand: U5P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2j4k.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2J4K; Ligand: U5P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2j4k.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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