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Receptor
PDB id Resolution Class Description Source Keywords
3BK2 2.1 Å EC: 3.-.-.- CRYSTAL STRUCTURE ANALYSIS OF THE RNASE J/UMP COMPLEX THERMUS THERMOPHILUS RNASE J ENDORIBONUCLEASE EXORIBONUCLEASE METAL DEPENDENT HYDROLASE METALLO-BETA-LACTAMASE HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE DUAL ACTIVITY OF RNASE NAT.STRUCT.MOL.BIOL. V. 15 206 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:601;
A:602;
A:603;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:947;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
U5P A:950;
 Valid;
 none;
 submit data
324.181 C9 H13 N2 O9 P C1=CN...
ZN A:948;
A:949;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3BK2 2.1 Å EC: 3.-.-.- CRYSTAL STRUCTURE ANALYSIS OF THE RNASE J/UMP COMPLEX THERMUS THERMOPHILUS RNASE J ENDORIBONUCLEASE EXORIBONUCLEASE METAL DEPENDENT HYDROLASE METALLO-BETA-LACTAMASE HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE DUAL ACTIVITY OF RNASE NAT.STRUCT.MOL.BIOL. V. 15 206 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 3T3O - OMC OMU OMG OMG U n/a n/a
2 3BK2 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 3T3O - OMC OMU OMG OMG U n/a n/a
2 3BK2 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
3 4XWT - 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 173 families.
1 3T3O - OMC OMU OMG OMG U n/a n/a
2 3BK2 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
3 4XWT - U5P C9 H13 N2 O9 P C1=CN(C(=O....
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 : 3BK2; Ligand: U5P; Similar sites found with APoc: 27
This union binding pocket(no: 1) in the query (biounit: 3bk2.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2NZ5 226 1.21065
2 4UTG ANP 1.7341
3 3MKN DNB 1.89873
4 4LZJ 22H 2.31023
5 1VEM GLC GLC 2.51938
6 1GAH ACR 2.76008
7 4GU5 FAD 2.96846
8 4LAX FK5 2.97398
9 3FPF MTA 3.02013
10 3FPF TNA 3.02013
11 2OKL BB2 3.24324
12 6AMI TRP 3.53535
13 6FK3 PPI 4.09253
14 5GWT NAD 4.31655
15 5GWT SIN 4.31655
16 4CS9 AMP 4.7619
17 1A99 PUT 4.94186
18 1SQL GUN 5.47945
19 4PTN PYR 5.8309
20 4X8O AP5 6.54206
21 2BNF UTP 6.639
22 2JFV FLC 8.24742
23 1CBK ROI 8.75
24 6GR0 F8W 16.6667
25 1NNU NAD 19.6507
26 1NNU TCT 19.6507
27 4AF5 CIT 23.6842
Pocket No.: 2; Query (leader) PDB : 3BK2; 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: 3bk2.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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