Receptor
PDB id Resolution Class Description Source Keywords
11BG 1.9 Å EC: 3.1.27.5 A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING SEMINAL RIBONUCLEASE BOS TAURUS HYDROLASE PHOSPHORIC DIESTER RNA
Ref.: A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN IN BOVINE SEMINAL RIBONUCLEASE. J.MOL.BIOL. V. 293 569 1999
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:125;
A:126;
A:128;
A:134;
A:135;
B:127;
B:129;
B:136;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
U2G A:130;
A:131;
A:132;
B:133;
Valid;
Valid;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0;
none;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
submit data
589.407 C19 H24 N7 O13 P c1nc2...
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 3DJV Ki = 27.9 uM C3P C9 H14 N3 O8 P C1=CN(C(=O....
2 1R5C - CPA C19 H25 N8 O9 P c1nc(c2c(n....
3 11BA - UPA C19 H24 N7 O12 P c1nc(c2c(n....
4 1TQ9 - CPA C19 H25 N8 O9 P c1nc(c2c(n....
5 3DJQ Ki = 1046.4 uM UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 3DJP Ki = 63.2 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
7 3DJX Ki = 1557 uM C5P C9 H14 N3 O8 P C1=CN(C(=O....
8 11BG - U2G C19 H24 N7 O13 P c1nc2c(n1[....
9 3DJO Ki = 40.8 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
10 1N3Z - U3P C9 H13 N2 O9 P C1=CN(C(=O....
70% Homology Family (67)
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 1W4O Ki = 5.85 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
4 1RNN - C5P C9 H14 N3 O8 P C1=CN(C(=O....
5 1JVU - C2P C9 H14 N3 O8 P C1=CN(C(=O....
6 3D7B Ki = 203 uM U4S C13 H19 N3 O5 C1CCN(C1)C....
7 3FL1 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
8 2XOG Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
9 3D6Q Ki = 172 uM U3S C14 H21 N3 O5 C1CCN(CC1)....
10 3JW1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
11 3EV6 - RSF C6 H10 O3 C1CO[C@H]2....
12 2W5I Ki = 4.7 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
13 3D8Y Ki = 396 uM T3S C15 H23 N3 O4 CC1=CN(C(=....
14 1W4P Ki = 18 uM UM3 C9 H13 N2 O8 P C1[C@@H]([....
15 3D6O Ki = 77 uM U1S C17 H25 N3 O7 CCOC(=O)C1....
16 1AFL Ki = 520 nM ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
17 3EV3 - TBU C4 H10 O CC(C)(C)O
18 3LXO Kd = 15 uM T3P C10 H15 N2 O8 P CC1=CN(C(=....
19 3RID - CGP C19 H25 N8 O10 P c1nc2c(n1[....
20 1O0O Ki = 8 uM A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
21 1RPF - C3P C9 H14 N3 O8 P C1=CN(C(=O....
22 3D6P Ki = 179 uM U2S C13 H19 N3 O6 C1COCCN1C[....
23 1RPG - CPA C19 H25 N8 O9 P c1nc(c2c(n....
24 4G8V Ki = 1.6 uM 0EY C12 H15 N5 O6 c1c(nnn1[C....
25 1RNC - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
26 1WBU - WBU C4 H5 N3 O2 C1=C(C(=O)....
27 1ROB - C2P C9 H14 N3 O8 P C1=CN(C(=O....
28 1W4Q Ki = 5.5 uM UMF C9 H12 F N2 O8 P C1=CN(C(=O....
29 4G8Y Ki = 25.8 uM 0FT C13 H17 N5 O6 CC1=CN(C(=....
30 1O0F Ki = 5 uM A3P C10 H15 N5 O10 P2 c1nc(c2c(n....
31 1JN4 Ki = 11.3 uM 139 C19 H25 N7 O14 P2 c1nc(c2c(n....
32 1O0N Ki = 82 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
33 3EV4 - ETF C2 H3 F3 O C(C(F)(F)F....
34 1RCA - CGP C19 H25 N8 O10 P c1nc2c(n1[....
35 1AFK Ki = 240 nM PAP C10 H16 N5 O13 P3 c1nc(c2c(n....
36 1RND - DGP C10 H14 N5 O7 P c1nc2c(n1[....
37 2XOI Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
38 1EOW - U2G C19 H24 N7 O13 P c1nc2c(n1[....
39 4RSK Kd = 47.4 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
40 1RCN - DA DT DA DA n/a n/a
41 1RNM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
42 2W5K Ki = 12 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
43 2G8R Ki = 103 uM N3E C15 H21 N3 O7 C1CN(CCC1C....
44 1U1B Kd = 16 nM PAX C20 H27 N7 O20 P4 CC1=CN(C(=....
45 1QHC Ki = 27 nM PUA C19 H27 N7 O20 P4 c1nc(c2c(n....
46 3FL0 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
47 1F0V - DC DG n/a n/a
48 2W5L Ki = 63 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
49 1RUV - UVC C9 H12 N2 O9 V C1=CN(C(=O....
50 1O0M Ki = 7.1 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
51 2QCA - DGP C10 H14 N5 O7 P c1nc2c(n1[....
52 1Z6S Ki = 63 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
53 3EV5 - TMO C3 H9 N O C[N+](C)(C....
54 4G90 Ki = 30.8 uM 0G0 C12 H14 F N5 O6 c1c(nnn1[C....
55 2W5G Ki = 0.86 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
56 3D8Z Ki = 423 uM TXS C14 H21 N3 O4 CC1=CN(C(=....
57 1EOS - U2G C19 H24 N7 O13 P c1nc2c(n1[....
58 3DJV Ki = 27.9 uM C3P C9 H14 N3 O8 P C1=CN(C(=O....
59 1R5C - CPA C19 H25 N8 O9 P c1nc(c2c(n....
60 11BA - UPA C19 H24 N7 O12 P c1nc(c2c(n....
61 1TQ9 - CPA C19 H25 N8 O9 P c1nc(c2c(n....
62 3DJQ Ki = 1046.4 uM UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
63 3DJP Ki = 63.2 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
64 3DJX Ki = 1557 uM C5P C9 H14 N3 O8 P C1=CN(C(=O....
65 11BG - U2G C19 H24 N7 O13 P c1nc2c(n1[....
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....
50% Homology Family (68)
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 1W4O Ki = 5.85 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
4 1RNN - C5P C9 H14 N3 O8 P C1=CN(C(=O....
5 1JVU - C2P C9 H14 N3 O8 P C1=CN(C(=O....
6 3D7B Ki = 203 uM U4S C13 H19 N3 O5 C1CCN(C1)C....
7 3FL1 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
8 2XOG Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
9 3D6Q Ki = 172 uM U3S C14 H21 N3 O5 C1CCN(CC1)....
10 3JW1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
11 3EV6 - RSF C6 H10 O3 C1CO[C@H]2....
12 2W5I Ki = 4.7 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
13 3D8Y Ki = 396 uM T3S C15 H23 N3 O4 CC1=CN(C(=....
14 1W4P Ki = 18 uM UM3 C9 H13 N2 O8 P C1[C@@H]([....
15 3D6O Ki = 77 uM U1S C17 H25 N3 O7 CCOC(=O)C1....
16 1AFL Ki = 520 nM ATR C10 H16 N5 O13 P3 c1nc(c2c(n....
17 3EV3 - TBU C4 H10 O CC(C)(C)O
18 3LXO Kd = 15 uM T3P C10 H15 N2 O8 P CC1=CN(C(=....
19 3RID - CGP C19 H25 N8 O10 P c1nc2c(n1[....
20 1O0O Ki = 8 uM A2P C10 H15 N5 O10 P2 c1nc(c2c(n....
21 1RPF - C3P C9 H14 N3 O8 P C1=CN(C(=O....
22 3D6P Ki = 179 uM U2S C13 H19 N3 O6 C1COCCN1C[....
23 1RPG - CPA C19 H25 N8 O9 P c1nc(c2c(n....
24 4G8V Ki = 1.6 uM 0EY C12 H15 N5 O6 c1c(nnn1[C....
25 1RNC - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
26 1WBU - WBU C4 H5 N3 O2 C1=C(C(=O)....
27 1ROB - C2P C9 H14 N3 O8 P C1=CN(C(=O....
28 1W4Q Ki = 5.5 uM UMF C9 H12 F N2 O8 P C1=CN(C(=O....
29 4G8Y Ki = 25.8 uM 0FT C13 H17 N5 O6 CC1=CN(C(=....
30 1O0F Ki = 5 uM A3P C10 H15 N5 O10 P2 c1nc(c2c(n....
31 1JN4 Ki = 11.3 uM 139 C19 H25 N7 O14 P2 c1nc(c2c(n....
32 1O0N Ki = 82 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
33 3EV4 - ETF C2 H3 F3 O C(C(F)(F)F....
34 1RCA - CGP C19 H25 N8 O10 P c1nc2c(n1[....
35 1AFK Ki = 240 nM PAP C10 H16 N5 O13 P3 c1nc(c2c(n....
36 1RND - DGP C10 H14 N5 O7 P c1nc2c(n1[....
37 2XOI Ki = 370 uM SFB C20 H28 N8 O11 S c1nc(c2c(n....
38 1EOW - U2G C19 H24 N7 O13 P c1nc2c(n1[....
39 4RSK Kd = 47.4 uM U3P C9 H13 N2 O9 P C1=CN(C(=O....
40 1RCN - DA DT DA DA n/a n/a
41 1RNM - C5P C9 H14 N3 O8 P C1=CN(C(=O....
42 2W5K Ki = 12 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
43 2G8R Ki = 103 uM N3E C15 H21 N3 O7 C1CN(CCC1C....
44 1U1B Kd = 16 nM PAX C20 H27 N7 O20 P4 CC1=CN(C(=....
45 1QHC Ki = 27 nM PUA C19 H27 N7 O20 P4 c1nc(c2c(n....
46 3FL0 - CGP C19 H25 N8 O10 P c1nc2c(n1[....
47 1F0V - DC DG n/a n/a
48 2W5L Ki = 63 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
49 1RUV - UVC C9 H12 N2 O9 V C1=CN(C(=O....
50 1O0M Ki = 7.1 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
51 2QCA - DGP C10 H14 N5 O7 P c1nc2c(n1[....
52 1Z6S Ki = 63 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
53 3EV5 - TMO C3 H9 N O C[N+](C)(C....
54 4G90 Ki = 30.8 uM 0G0 C12 H14 F N5 O6 c1c(nnn1[C....
55 2W5G Ki = 0.86 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
56 3D8Z Ki = 423 uM TXS C14 H21 N3 O4 CC1=CN(C(=....
57 1EOS - U2G C19 H24 N7 O13 P c1nc2c(n1[....
58 2RNF - UM3 C9 H13 N2 O8 P C1[C@@H]([....
59 3DJV Ki = 27.9 uM C3P C9 H14 N3 O8 P C1=CN(C(=O....
60 1R5C - CPA C19 H25 N8 O9 P c1nc(c2c(n....
61 11BA - UPA C19 H24 N7 O12 P c1nc(c2c(n....
62 1TQ9 - CPA C19 H25 N8 O9 P c1nc(c2c(n....
63 3DJQ Ki = 1046.4 uM UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
64 3DJP Ki = 63.2 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
65 3DJX Ki = 1557 uM C5P C9 H14 N3 O8 P C1=CN(C(=O....
66 11BG - U2G C19 H24 N7 O13 P c1nc2c(n1[....
67 3DJO Ki = 40.8 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
68 1N3Z - U3P C9 H13 N2 O9 P C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: U2G; Similar ligands found: 100
No: Ligand ECFP6 Tc MDL keys Tc
1 U2G 1 1
2 CG2 0.8 1
3 GPG 0.707547 0.95
4 UPA 0.686957 0.925
5 GDP 0.634615 0.936709
6 GNH 0.628571 0.925
7 GP3 0.625 0.9375
8 GSP 0.62037 0.891566
9 G 0.617647 0.924051
10 5GP 0.617647 0.924051
11 GTP 0.616822 0.936709
12 GDD 0.608696 0.95
13 GKE 0.608696 0.95
14 GDC 0.608696 0.95
15 GMV 0.601852 0.91358
16 G1R 0.59633 0.925
17 GCP 0.59633 0.91358
18 G2R 0.59292 0.902439
19 GNP 0.590909 0.91358
20 GAV 0.580357 0.902439
21 GKD 0.575 0.95
22 GP2 0.574074 0.902439
23 U G A 0.571429 0.950617
24 GPC 0.565891 0.939759
25 G U34 0.563492 0.950617
26 GDR 0.563025 0.925926
27 GFB 0.563025 0.925926
28 G2P 0.5625 0.902439
29 JB2 0.561983 0.925926
30 GDP MG 0.54955 0.86747
31 YGP 0.546219 0.915663
32 G3A 0.545455 0.9375
33 GDX 0.544715 0.9375
34 ALF 5GP 0.544643 0.837209
35 Y9Z 0.541667 0.872093
36 G5P 0.540984 0.9375
37 GMP 0.54 0.848101
38 GTG 0.53719 0.903614
39 JB3 0.535433 0.914634
40 GPD 0.532258 0.892857
41 GTP MG 0.530435 0.86747
42 BEF GDP 0.530435 0.837209
43 G4P 0.525862 0.924051
44 GCP G 0.525862 0.878049
45 0O2 0.521008 0.924051
46 FEG 0.51938 0.850575
47 G C 0.519084 0.9625
48 TPG 0.518248 0.855556
49 GDP AF3 0.516949 0.837209
50 GDP ALF 0.516949 0.837209
51 G G 0.512195 0.91358
52 2GP 0.509259 0.924051
53 3GP 0.509259 0.911392
54 G3D 0.508621 0.924051
55 NGD 0.507692 0.925926
56 2MD 0.507576 0.905882
57 CAG 0.507463 0.852273
58 FE9 0.49635 0.791667
59 MGD 0.496296 0.905882
60 OMC OMU OMG OMG U 0.493243 0.904762
61 G G G RPC 0.485075 0.91358
62 UPU 0.482143 0.822785
63 4TC 0.480916 0.890244
64 U2P 0.480392 0.810127
65 GDP 7MG 0.480315 0.879518
66 APU 0.477273 0.9125
67 UP5 0.476923 0.9125
68 MD1 0.471429 0.905882
69 PGD 0.471429 0.915663
70 G A A A 0.470588 0.91358
71 DBG 0.464789 0.914634
72 G G G C 0.464286 0.950617
73 P2G 0.460177 0.851852
74 G C C C 0.458333 0.9625
75 G4M 0.453333 0.873563
76 I2C FE2 CMO CMO 0.45 0.824176
77 GPX 0.447154 0.8875
78 G1G 0.446809 0.892857
79 139 0.437956 0.891566
80 3PD UM3 0.437956 0.903614
81 CGP 0.434783 0.927711
82 PUP 0.434426 0.780488
83 PGD O 0.431507 0.865169
84 DGI 0.428571 0.86747
85 P1G 0.42735 0.841463
86 DGT 0.42623 0.86747
87 G1R G1R 0.424658 0.891566
88 IDP 0.423729 0.911392
89 G G U 0.421053 0.901235
90 BGO 0.42029 0.891566
91 DG 0.413793 0.855422
92 DGP 0.413793 0.855422
93 A U 0.413043 0.888889
94 UDP 0.410714 0.822785
95 DA DU DG DA 0.410072 0.848837
96 IMP 0.405172 0.898734
97 GGM 0.401408 0.870588
98 CSV 0.4 0.841463
99 UTP 0.4 0.822785
100 CSQ 0.4 0.841463
Similar Binding Sites
Pocket no: 1; Query (leader) PDB : 3DJV; Ligand: C3P; Similar sites found: 24
This union binding pocket (no: 1) in the query (biounit: 3djv.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 3DJV C3P 8.872e-20 1
2 1U1B PAX 1.123e-11 0.71543
3 2BZZ AP5 3.229e-07 0.46186
4 2RNF UM3 2.129e-09 0.42952
5 1M07 DC 2.211e-08 0.40848
6 2GMK AMP 3.296e-07 0.3975
7 2Q4G CIT 1.643e-05 0.32562
8 4MZQ 1VU 0.03012 0.31585
9 3P48 DUP 0.04429 0.30272
10 3UKR CKH 0.04306 0.29039
11 2A9W UMP 0.03825 0.28701
12 2HRL SIA 0.03836 0.28492
13 2WBV SIA 0.03074 0.28385
14 2Q2R BGC 0.0467 0.28357
15 2WBV SIA 0.04131 0.28304
16 4NS0 PIO 0.03772 0.27653
17 4X0M 3WA 0.04937 0.27604
18 2R5A MLZ 0.04 0.2751
19 2QLU ADE 0.047 0.27378
20 1JPA ANP 0.01072 0.27361
21 1WOG 16D 0.04242 0.27067
22 2RHI THR 0.04691 0.27051
23 1SS4 GSH 0.03719 0.25819
24 1XVB BBU 0.007607 0.25773
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