Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C3P A:125;
B:201;
Valid;
Valid;
none;
none;
Ki = 27.9 uM
323.197 C9 H14 N3 O8 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 (79)
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 6PVW Ki = 0.48 uM OZV C10 H16 N5 O18 P5 c1nc(c2c(n....
7 3D6Q Ki = 172 uM U3S C14 H21 N3 O5 C1CCN(CC1)....
8 3JW1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
9 3EV6 - RSF C6 H10 O3 C1CO[C@H]2....
10 2W5I Ki = 4.7 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 3D8Y Ki = 396 uM T3S C15 H23 N3 O4 CC1=CN(C(=....
12 3D6O Ki = 77 uM U1S C17 H25 N3 O7 CCOC(=O)C1....
13 3LXO Kd = 15 uM T3P C10 H15 N2 O8 P CC1=CN(C(=....
14 1O0O Ki = 8 uM A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
15 1RPF - C3P C9 H14 N3 O8 P C1=CN(C(=O....
16 3D6P Ki = 179 uM U2S C13 H19 N3 O6 C1COCCN1C[....
17 4G8V Ki = 1.6 uM 0EY C12 H15 N5 O6 c1c(nnn1[C....
18 1RNC - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
19 4WYZ Kd = 50 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
20 1ROB - C2P C9 H14 N3 O8 P C1=CN(C(=O....
21 1W4Q Ki = 5.5 uM UMF C9 H12 F N2 O8 P C1=CN(C(=O....
22 6PVV Ki = 1.4 uM 5FA C10 H18 N5 O19 P5 c1nc(c2c(n....
23 1O0F Ki = 5 uM A3P C10 H15 N5 O10 P2 c1nc(c2c(n....
24 3EV4 - ETF C2 H3 F3 O C(C(F)(F)F....
25 1RCA - CGP C19 H25 N8 O10 P c1nc2c(n1[....
26 1RND - DGP C10 H14 N5 O7 P c1nc2c(n1[....
27 4RSK Kd = 47.4 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
28 1RCN - DA DT DA DA n/a n/a
29 6PVX Ki = 0.068 uM U5F C9 H17 N2 O21 P5 C1=CN(C(=O....
30 1RNM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
31 2W5K Ki = 12 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
32 2G8R Ki = 103 uM N3E C15 H21 N3 O7 C1CN(CCC1C....
33 1U1B Kd = 16 nM PAX C20 H27 N7 O20 P4 CC1=CN(C(=....
34 1QHC Ki = 27 nM PUA C19 H27 N7 O20 P4 c1nc(c2c(n....
35 3FL0 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
36 4WYP Kd = 440 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
37 1O0M Ki = 7.1 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
38 2QCA - DGP C10 H14 N5 O7 P c1nc2c(n1[....
39 3EV5 - TMO C3 H9 N O C[N+](C)(C....
40 4S18 - 1PT C6 H14 N2 Pt C1CC[C@@H]....
41 1EOS - U2G C19 H24 N7 O13 P c1nc2c(n1[....
42 4RTE - CPT Cl2 H6 N2 Pt [NH3][Pt](....
43 1W4O Ki = 5.85 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
44 1RNN - C5P C9 H14 N3 O8 P C1=CN(C(=O....
45 2XOG Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
46 1W4P Ki = 18 uM UM3 C9 H13 N2 O8 P C1[C@@H]([....
47 1AFL Ki = 520 nM ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
48 3EV3 - TBU C4 H10 O CC(C)(C)O
49 3RID - CGP C19 H25 N8 O10 P c1nc2c(n1[....
50 1RPG - CPA C19 H25 N8 O9 P c1nc(c2c(n....
51 1WBU - WBU C4 H5 N3 O2 C1=C(C(=O)....
52 6QE9 - J9H C17 H18 N3 Pt Cc1ccc2ccc....
53 4G8Y Ki = 25.8 uM 0FT C13 H17 N5 O6 CC1=CN(C(=....
54 1JN4 Ki = 11.3 uM 139 C19 H25 N7 O14 P2 c1nc(c2c(n....
55 1O0N Ki = 82 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
56 1AFK Ki = 240 nM PAP C10 H16 N5 O13 P3 c1nc(c2c(n....
57 2XOI Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
58 1EOW - U2G C19 H24 N7 O13 P c1nc2c(n1[....
59 5OGH - C3P C9 H14 N3 O8 P C1=CN(C(=O....
60 5NA9 - QPT C6 H12 N2 O4 Pt C1CC2(C1)C....
61 1F0V - DC DG n/a n/a
62 2W5L Ki = 63 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
63 1RUV - UVC C9 H12 N2 O9 V C1=CN(C(=O....
64 1Z6S Ki = 63 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
65 4G90 Ki = 30.8 uM 0G0 C12 H14 F N5 O6 c1c(nnn1[C....
66 6F60 - DVW C27 H31 N7 O5 Pt CC1=CC=C2C....
67 2W5G Ki = 0.86 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
68 3D8Z Ki = 423 uM TXS C14 H21 N3 O4 CC1=CN(C(=....
69 5JLG - RU Ru [Ru+3]
70 11BA - UPA C19 H24 N7 O12 P c1nc(c2c(n....
71 1TQ9 - CPA C19 H25 N8 O9 P c1nc(c2c(n....
72 3DJO Ki = 40.8 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
73 1N3Z - U3P C9 H13 N2 O9 P C1=CN(C(=O....
74 3DJV Ki = 27.9 uM C3P C9 H14 N3 O8 P C1=CN(C(=O....
75 1R5C - CPA C19 H25 N8 O9 P c1nc(c2c(n....
76 3DJQ Ki = 1046.4 uM UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
77 3DJP Ki = 63.2 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
78 3DJX Ki = 1557 uM C5P C9 H14 N3 O8 P C1=CN(C(=O....
79 11BG - U2G C19 H24 N7 O13 P c1nc2c(n1[....
50% Homology Family (81)
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 6PVW Ki = 0.48 uM OZV C10 H16 N5 O18 P5 c1nc(c2c(n....
7 3D6Q Ki = 172 uM U3S C14 H21 N3 O5 C1CCN(CC1)....
8 3JW1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
9 3EV6 - RSF C6 H10 O3 C1CO[C@H]2....
10 2W5I Ki = 4.7 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 3D8Y Ki = 396 uM T3S C15 H23 N3 O4 CC1=CN(C(=....
12 3D6O Ki = 77 uM U1S C17 H25 N3 O7 CCOC(=O)C1....
13 3LXO Kd = 15 uM T3P C10 H15 N2 O8 P CC1=CN(C(=....
14 1O0O Ki = 8 uM A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
15 1RPF - C3P C9 H14 N3 O8 P C1=CN(C(=O....
16 3D6P Ki = 179 uM U2S C13 H19 N3 O6 C1COCCN1C[....
17 4G8V Ki = 1.6 uM 0EY C12 H15 N5 O6 c1c(nnn1[C....
18 1RNC - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
19 4WYZ Kd = 50 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
20 1ROB - C2P C9 H14 N3 O8 P C1=CN(C(=O....
21 1W4Q Ki = 5.5 uM UMF C9 H12 F N2 O8 P C1=CN(C(=O....
22 6PVV Ki = 1.4 uM 5FA C10 H18 N5 O19 P5 c1nc(c2c(n....
23 1O0F Ki = 5 uM A3P C10 H15 N5 O10 P2 c1nc(c2c(n....
24 3EV4 - ETF C2 H3 F3 O C(C(F)(F)F....
25 1RCA - CGP C19 H25 N8 O10 P c1nc2c(n1[....
26 1RND - DGP C10 H14 N5 O7 P c1nc2c(n1[....
27 4RSK Kd = 47.4 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
28 1RCN - DA DT DA DA n/a n/a
29 6PVX Ki = 0.068 uM U5F C9 H17 N2 O21 P5 C1=CN(C(=O....
30 1RNM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
31 2W5K Ki = 12 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
32 2G8R Ki = 103 uM N3E C15 H21 N3 O7 C1CN(CCC1C....
33 1U1B Kd = 16 nM PAX C20 H27 N7 O20 P4 CC1=CN(C(=....
34 1QHC Ki = 27 nM PUA C19 H27 N7 O20 P4 c1nc(c2c(n....
35 3FL0 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
36 4WYP Kd = 440 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
37 1O0M Ki = 7.1 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
38 2QCA - DGP C10 H14 N5 O7 P c1nc2c(n1[....
39 3EV5 - TMO C3 H9 N O C[N+](C)(C....
40 4S18 - 1PT C6 H14 N2 Pt C1CC[C@@H]....
41 1EOS - U2G C19 H24 N7 O13 P c1nc2c(n1[....
42 4RTE - CPT Cl2 H6 N2 Pt [NH3][Pt](....
43 1W4O Ki = 5.85 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
44 1RNN - C5P C9 H14 N3 O8 P C1=CN(C(=O....
45 2XOG Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
46 1W4P Ki = 18 uM UM3 C9 H13 N2 O8 P C1[C@@H]([....
47 1AFL Ki = 520 nM ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
48 3EV3 - TBU C4 H10 O CC(C)(C)O
49 3RID - CGP C19 H25 N8 O10 P c1nc2c(n1[....
50 1RPG - CPA C19 H25 N8 O9 P c1nc(c2c(n....
51 1WBU - WBU C4 H5 N3 O2 C1=C(C(=O)....
52 6QE9 - J9H C17 H18 N3 Pt Cc1ccc2ccc....
53 4G8Y Ki = 25.8 uM 0FT C13 H17 N5 O6 CC1=CN(C(=....
54 1JN4 Ki = 11.3 uM 139 C19 H25 N7 O14 P2 c1nc(c2c(n....
55 1O0N Ki = 82 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
56 1AFK Ki = 240 nM PAP C10 H16 N5 O13 P3 c1nc(c2c(n....
57 2XOI Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
58 1EOW - U2G C19 H24 N7 O13 P c1nc2c(n1[....
59 5OGH - C3P C9 H14 N3 O8 P C1=CN(C(=O....
60 5NA9 - QPT C6 H12 N2 O4 Pt C1CC2(C1)C....
61 1F0V - DC DG n/a n/a
62 2W5L Ki = 63 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
63 1RUV - UVC C9 H12 N2 O9 V C1=CN(C(=O....
64 1Z6S Ki = 63 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
65 4G90 Ki = 30.8 uM 0G0 C12 H14 F N5 O6 c1c(nnn1[C....
66 6F60 - DVW C27 H31 N7 O5 Pt CC1=CC=C2C....
67 2W5G Ki = 0.86 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
68 3D8Z Ki = 423 uM TXS C14 H21 N3 O4 CC1=CN(C(=....
69 5JLG - RU Ru [Ru+3]
70 11BA - UPA C19 H24 N7 O12 P c1nc(c2c(n....
71 1TQ9 - CPA C19 H25 N8 O9 P c1nc(c2c(n....
72 3DJO Ki = 40.8 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
73 1N3Z - U3P C9 H13 N2 O9 P C1=CN(C(=O....
74 3DJV Ki = 27.9 uM C3P C9 H14 N3 O8 P C1=CN(C(=O....
75 1R5C - CPA C19 H25 N8 O9 P c1nc(c2c(n....
76 3DJQ Ki = 1046.4 uM UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
77 3DJP Ki = 63.2 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
78 3DJX Ki = 1557 uM C5P C9 H14 N3 O8 P C1=CN(C(=O....
79 11BG - U2G C19 H24 N7 O13 P c1nc2c(n1[....
80 5ARK - UMP C9 H13 N2 O8 P C1[C@@H]([....
81 2RNF - UM3 C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C3P; Similar ligands found: 44
No: Ligand ECFP6 Tc MDL keys Tc
1 C3P 1 1
2 C2P 0.692308 0.956522
3 AR3 0.655738 0.828571
4 CTN 0.655738 0.828571
5 C C C C 0.617284 0.915493
6 DKZ 0.597015 0.743243
7 C5P 0.585714 0.956522
8 C 0.585714 0.956522
9 CAR 0.585714 0.956522
10 UA3 0.565217 0.940298
11 U3P 0.565217 0.940298
12 CSV 0.561798 0.90411
13 CSQ 0.561798 0.90411
14 CDP 0.56 0.942857
15 I5A 0.545455 0.788732
16 C C 0.542169 0.901408
17 CTP 0.538462 0.942857
18 HF4 0.538462 0.942857
19 2TM 0.525 0.90411
20 7XL 0.512195 0.916667
21 C5G 0.511364 0.916667
22 C2G 0.494118 0.929577
23 0RC 0.493976 0.891892
24 CDM 0.483146 0.868421
25 CDC 0.47191 0.802469
26 LDC 0.457143 0.780822
27 DCZ 0.457143 0.780822
28 CXY 0.456522 0.890411
29 DC 0.448718 0.888889
30 DCM 0.448718 0.888889
31 GEO 0.444444 0.780822
32 A C A C 0.441441 0.833333
33 CTP C C C C 0.441176 0.942029
34 U A C C 0.428571 0.820513
35 YYY 0.421687 0.876712
36 G C 0.418182 0.835443
37 G G G RPC 0.418182 0.833333
38 GPC 0.40708 0.817073
39 GCQ 0.406977 0.876712
40 1AA 0.405941 0.855263
41 DOC 0.405063 0.888889
42 U2P 0.402597 0.898551
43 CC7 0.402439 0.887324
44 DCP 0.402299 0.876712
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DJV; Ligand: C3P; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 3djv.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
1 2GMK AMP 32.6923
Pocket No.: 2; Query (leader) PDB : 3DJV; Ligand: C3P; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 3djv.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
1 2GMK AMP 32.6923
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