Receptor
PDB id Resolution Class Description Source Keywords
3djo 1.6 Å EC: 3.1.27.5 BOVINE SEMINAL RIBONUCLEASE URIDINE 2' PHOSPHATE COMPLEX BOS TAURUS RIBONUCLEASE HYDROLASE ALLOSTERIC ENZYME ENDONUCLEASE NUSECRETED
Ref.: MAPPING THE RIBONUCLEOLYTIC ACTIVE SITE OF BOVINE S RIBONUCLEASE. THE BINDING OF PYRIMIDINYL PHOSPHONUC INHIBITORS EUR.J.MED.CHEM. V. 44 4496 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT B:301;
B:302;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
U2P A:125;
B:201;
Valid;
Valid;
none;
none;
Ki = 40.8 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
3DJV 1.6 Å EC: 3.1.27.5 BOVINE SEMINAL RIBONUCLEASE- CYTIDINE 3' PHOSPHATE COMPLEX BOS TAURUS RIBONUCLEASE HYDROLASE ALLOSTERIC ENZYME ENDONUCLEASE NUSECRETED
Ref.: MAPPING THE RIBONUCLEOLYTIC ACTIVE SITE OF BOVINE S RIBONUCLEASE. THE BINDING OF PYRIMIDINYL PHOSPHONUC INHIBITORS EUR.J.MED.CHEM. V. 44 4496 2009
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 11BA - UPA C19 H24 N7 O12 P c1nc(c2c(n....
2 1TQ9 - CPA C19 H25 N8 O9 P c1nc(c2c(n....
3 3DJO Ki = 40.8 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
4 1N3Z - U3P C9 H13 N2 O9 P C1=CN(C(=O....
5 3DJV Ki = 27.9 uM C3P C9 H14 N3 O8 P C1=CN(C(=O....
6 1R5C - CPA C19 H25 N8 O9 P c1nc(c2c(n....
7 3DJQ Ki = 1046.4 uM UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
8 3DJP Ki = 63.2 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
9 3DJX Ki = 1557 uM C5P C9 H14 N3 O8 P C1=CN(C(=O....
10 11BG - U2G C19 H24 N7 O13 P c1nc2c(n1[....
70% Homology Family (73)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1Z6D Ki = 4.6 mM IMP C10 H13 N4 O8 P c1nc2c(n1[....
2 1O0H Ki = 1.2 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 1JVU - C2P C9 H14 N3 O8 P C1=CN(C(=O....
4 3D7B Ki = 203 uM U4S C13 H19 N3 O5 C1CCN(C1)C....
5 3FL1 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
6 3D6Q Ki = 172 uM U3S C14 H21 N3 O5 C1CCN(CC1)....
7 3JW1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
8 3EV6 - RSF C6 H10 O3 C1CO[C@H]2....
9 2W5I Ki = 4.7 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
10 3D8Y Ki = 396 uM T3S C15 H23 N3 O4 CC1=CN(C(=....
11 3D6O Ki = 77 uM U1S C17 H25 N3 O7 CCOC(=O)C1....
12 3LXO Kd = 15 uM T3P C10 H15 N2 O8 P CC1=CN(C(=....
13 1O0O Ki = 8 uM A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
14 1RPF - C3P C9 H14 N3 O8 P C1=CN(C(=O....
15 3D6P Ki = 179 uM U2S C13 H19 N3 O6 C1COCCN1C[....
16 4G8V Ki = 1.6 uM 0EY C12 H15 N5 O6 c1c(nnn1[C....
17 1RNC - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
18 4WYZ Kd = 50 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
19 1ROB - C2P C9 H14 N3 O8 P C1=CN(C(=O....
20 1W4Q Ki = 5.5 uM UMF C9 H12 F N2 O8 P C1=CN(C(=O....
21 1O0F Ki = 5 uM A3P C10 H15 N5 O10 P2 c1nc(c2c(n....
22 3EV4 - ETF C2 H3 F3 O C(C(F)(F)F....
23 1RCA - CGP C19 H25 N8 O10 P c1nc2c(n1[....
24 1RND - DGP C10 H14 N5 O7 P c1nc2c(n1[....
25 4RSK Kd = 47.4 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
26 1RCN - DA DT DA DA n/a n/a
27 1RNM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
28 2W5K Ki = 12 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
29 2G8R Ki = 103 uM N3E C15 H21 N3 O7 C1CN(CCC1C....
30 1U1B Kd = 16 nM PAX C20 H27 N7 O20 P4 CC1=CN(C(=....
31 1QHC Ki = 27 nM PUA C19 H27 N7 O20 P4 c1nc(c2c(n....
32 3FL0 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
33 4WYP Kd = 440 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
34 1O0M Ki = 7.1 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
35 2QCA - DGP C10 H14 N5 O7 P c1nc2c(n1[....
36 3EV5 - TMO C3 H9 N O C[N+](C)(C....
37 4S18 - 1PT C6 H14 N2 Pt C1CC[C@@H]....
38 1EOS - U2G C19 H24 N7 O13 P c1nc2c(n1[....
39 4RTE - CPT Cl2 H6 N2 Pt [NH3][Pt](....
40 1W4O Ki = 5.85 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
41 1RNN - C5P C9 H14 N3 O8 P C1=CN(C(=O....
42 2XOG Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
43 1W4P Ki = 18 uM UM3 C9 H13 N2 O8 P C1[C@@H]([....
44 1AFL Ki = 520 nM ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
45 3EV3 - TBU C4 H10 O CC(C)(C)O
46 3RID - CGP C19 H25 N8 O10 P c1nc2c(n1[....
47 1RPG - CPA C19 H25 N8 O9 P c1nc(c2c(n....
48 1WBU - WBU C4 H5 N3 O2 C1=C(C(=O)....
49 4G8Y Ki = 25.8 uM 0FT C13 H17 N5 O6 CC1=CN(C(=....
50 1JN4 Ki = 11.3 uM 139 C19 H25 N7 O14 P2 c1nc(c2c(n....
51 1O0N Ki = 82 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
52 1AFK Ki = 240 nM PAP C10 H16 N5 O13 P3 c1nc(c2c(n....
53 2XOI Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
54 1EOW - U2G C19 H24 N7 O13 P c1nc2c(n1[....
55 5NA9 - QPT C6 H12 N2 O4 Pt C1CC2(C1)C....
56 1F0V - DC DG n/a n/a
57 2W5L Ki = 63 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
58 1RUV - UVC C9 H12 N2 O9 V C1=CN(C(=O....
59 1Z6S Ki = 63 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
60 4G90 Ki = 30.8 uM 0G0 C12 H14 F N5 O6 c1c(nnn1[C....
61 2W5G Ki = 0.86 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
62 3D8Z Ki = 423 uM TXS C14 H21 N3 O4 CC1=CN(C(=....
63 5JLG - RU Ru [Ru+3]
64 11BA - UPA C19 H24 N7 O12 P c1nc(c2c(n....
65 1TQ9 - CPA C19 H25 N8 O9 P c1nc(c2c(n....
66 3DJO Ki = 40.8 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
67 1N3Z - U3P C9 H13 N2 O9 P C1=CN(C(=O....
68 3DJV Ki = 27.9 uM C3P C9 H14 N3 O8 P C1=CN(C(=O....
69 1R5C - CPA C19 H25 N8 O9 P c1nc(c2c(n....
70 3DJQ Ki = 1046.4 uM UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
71 3DJP Ki = 63.2 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
72 3DJX Ki = 1557 uM C5P C9 H14 N3 O8 P C1=CN(C(=O....
73 11BG - U2G C19 H24 N7 O13 P c1nc2c(n1[....
50% Homology Family (75)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1Z6D Ki = 4.6 mM IMP C10 H13 N4 O8 P c1nc2c(n1[....
2 1O0H Ki = 1.2 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 1JVU - C2P C9 H14 N3 O8 P C1=CN(C(=O....
4 3D7B Ki = 203 uM U4S C13 H19 N3 O5 C1CCN(C1)C....
5 3FL1 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
6 3D6Q Ki = 172 uM U3S C14 H21 N3 O5 C1CCN(CC1)....
7 3JW1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
8 3EV6 - RSF C6 H10 O3 C1CO[C@H]2....
9 2W5I Ki = 4.7 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
10 3D8Y Ki = 396 uM T3S C15 H23 N3 O4 CC1=CN(C(=....
11 3D6O Ki = 77 uM U1S C17 H25 N3 O7 CCOC(=O)C1....
12 3LXO Kd = 15 uM T3P C10 H15 N2 O8 P CC1=CN(C(=....
13 1O0O Ki = 8 uM A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
14 1RPF - C3P C9 H14 N3 O8 P C1=CN(C(=O....
15 3D6P Ki = 179 uM U2S C13 H19 N3 O6 C1COCCN1C[....
16 4G8V Ki = 1.6 uM 0EY C12 H15 N5 O6 c1c(nnn1[C....
17 1RNC - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
18 4WYZ Kd = 50 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
19 1ROB - C2P C9 H14 N3 O8 P C1=CN(C(=O....
20 1W4Q Ki = 5.5 uM UMF C9 H12 F N2 O8 P C1=CN(C(=O....
21 1O0F Ki = 5 uM A3P C10 H15 N5 O10 P2 c1nc(c2c(n....
22 3EV4 - ETF C2 H3 F3 O C(C(F)(F)F....
23 1RCA - CGP C19 H25 N8 O10 P c1nc2c(n1[....
24 1RND - DGP C10 H14 N5 O7 P c1nc2c(n1[....
25 4RSK Kd = 47.4 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
26 1RCN - DA DT DA DA n/a n/a
27 1RNM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
28 2W5K Ki = 12 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
29 2G8R Ki = 103 uM N3E C15 H21 N3 O7 C1CN(CCC1C....
30 1U1B Kd = 16 nM PAX C20 H27 N7 O20 P4 CC1=CN(C(=....
31 1QHC Ki = 27 nM PUA C19 H27 N7 O20 P4 c1nc(c2c(n....
32 3FL0 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
33 4WYP Kd = 440 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
34 1O0M Ki = 7.1 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
35 2QCA - DGP C10 H14 N5 O7 P c1nc2c(n1[....
36 3EV5 - TMO C3 H9 N O C[N+](C)(C....
37 4S18 - 1PT C6 H14 N2 Pt C1CC[C@@H]....
38 1EOS - U2G C19 H24 N7 O13 P c1nc2c(n1[....
39 4RTE - CPT Cl2 H6 N2 Pt [NH3][Pt](....
40 1W4O Ki = 5.85 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
41 1RNN - C5P C9 H14 N3 O8 P C1=CN(C(=O....
42 2XOG Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
43 1W4P Ki = 18 uM UM3 C9 H13 N2 O8 P C1[C@@H]([....
44 1AFL Ki = 520 nM ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
45 3EV3 - TBU C4 H10 O CC(C)(C)O
46 3RID - CGP C19 H25 N8 O10 P c1nc2c(n1[....
47 1RPG - CPA C19 H25 N8 O9 P c1nc(c2c(n....
48 1WBU - WBU C4 H5 N3 O2 C1=C(C(=O)....
49 4G8Y Ki = 25.8 uM 0FT C13 H17 N5 O6 CC1=CN(C(=....
50 1JN4 Ki = 11.3 uM 139 C19 H25 N7 O14 P2 c1nc(c2c(n....
51 1O0N Ki = 82 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
52 1AFK Ki = 240 nM PAP C10 H16 N5 O13 P3 c1nc(c2c(n....
53 2XOI Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
54 1EOW - U2G C19 H24 N7 O13 P c1nc2c(n1[....
55 5NA9 - QPT C6 H12 N2 O4 Pt C1CC2(C1)C....
56 1F0V - DC DG n/a n/a
57 2W5L Ki = 63 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
58 1RUV - UVC C9 H12 N2 O9 V C1=CN(C(=O....
59 1Z6S Ki = 63 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
60 4G90 Ki = 30.8 uM 0G0 C12 H14 F N5 O6 c1c(nnn1[C....
61 2W5G Ki = 0.86 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
62 3D8Z Ki = 423 uM TXS C14 H21 N3 O4 CC1=CN(C(=....
63 5JLG - RU Ru [Ru+3]
64 11BA - UPA C19 H24 N7 O12 P c1nc(c2c(n....
65 1TQ9 - CPA C19 H25 N8 O9 P c1nc(c2c(n....
66 3DJO Ki = 40.8 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
67 1N3Z - U3P C9 H13 N2 O9 P C1=CN(C(=O....
68 3DJV Ki = 27.9 uM C3P C9 H14 N3 O8 P C1=CN(C(=O....
69 1R5C - CPA C19 H25 N8 O9 P c1nc(c2c(n....
70 3DJQ Ki = 1046.4 uM UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
71 3DJP Ki = 63.2 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
72 3DJX Ki = 1557 uM C5P C9 H14 N3 O8 P C1=CN(C(=O....
73 11BG - U2G C19 H24 N7 O13 P c1nc2c(n1[....
74 5ARK - UMP C9 H13 N2 O8 P C1[C@@H]([....
75 2RNF - UM3 C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: U2P; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 U2P 1 1
2 U3P 0.68254 0.953846
3 UA3 0.68254 0.953846
4 UMF 0.621212 0.897059
5 U 0.590164 0.848485
6 URI 0.590164 0.848485
7 CJB 0.587302 0.80597
8 C2P 0.565217 0.941176
9 DKX 0.537313 0.782609
10 U5P 0.528571 0.939394
11 UPU 0.5125 0.925373
12 PUP 0.511628 0.926471
13 UDP 0.506667 0.954545
14 UM3 0.492958 0.897059
15 UPA 0.49 0.828947
16 UTP 0.487179 0.954545
17 44P 0.486486 0.913043
18 U2G 0.480392 0.810127
19 UDP GAL 0.477273 0.898551
20 UPG 0.476744 0.926471
21 UFM 0.476744 0.926471
22 GDU 0.476744 0.926471
23 GUD 0.476744 0.926471
24 2KH 0.4625 0.926471
25 N3E 0.461538 0.743243
26 UPF 0.460674 0.875
27 U2F 0.460674 0.875
28 URM 0.45977 0.913043
29 660 0.45977 0.913043
30 Y6W 0.454545 0.875
31 UVC 0.452055 0.869565
32 UNP 0.451219 0.926471
33 UDP UDP 0.448718 0.895522
34 UFG 0.444444 0.875
35 UTP U U U 0.443182 0.880597
36 DUR 0.441176 0.797101
37 U4S 0.44 0.716216
38 UMP 0.434211 0.884058
39 DU 0.434211 0.884058
40 U U U U 0.431818 0.925373
41 U3S 0.428571 0.716216
42 U2S 0.428571 0.72973
43 CSQ 0.427083 0.837838
44 CSV 0.427083 0.837838
45 3UC 0.425532 0.875
46 UUA 0.42029 0.757576
47 UD1 0.418367 0.913043
48 UD2 0.418367 0.913043
49 U U 0.417582 0.911765
50 UDH 0.41573 0.851351
51 UPP 0.41573 0.898551
52 APU 0.415094 0.84
53 2TU 0.414286 0.760563
54 UAD 0.413043 0.898551
55 UDX 0.413043 0.898551
56 UDM 0.412371 0.9
57 DUD 0.407407 0.898551
58 USQ 0.404255 0.78481
59 UGA 0.404255 0.911765
60 UGB 0.404255 0.911765
61 C3P 0.402597 0.898551
62 G3N 0.4 0.873239
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DJV; Ligand: C3P; 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: 3djv.bio1) has 49 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3DJV; Ligand: C3P; Similar sites found: 7
This union binding pocket(no: 2) in the query (biounit: 3djv.bio1) has 51 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2YMZ LAT 0.007492 0.47427 None
2 5E89 TD2 0.04583 0.4016 None
3 1KJ1 MAN 0.03921 0.43185 1.83486
4 4WVW SLT 0.0483 0.41305 4.03226
5 1A78 TDG 0.01576 0.44946 4.83871
6 5DG2 GAL GLC 0.007276 0.4809 11.2903
7 2GMK AMP 0.0000003466 0.82601 32.6923
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