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Receptor
PDB id Resolution Class Description Source Keywords
2RNF 2.4 Å EC: 3.1.27.- X-RAY CRYSTAL STRUCTURE OF HUMAN RIBONUCLEASE 4 IN COMPLEX WITH D(UP) HOMO SAPIENS RIBONUCLEASE HYDROLASE PHOSPHODIESTERASE
Ref.: THE THREE-DIMENSIONAL STRUCTURE OF HUMAN RNASE 4, UNLIGANDED AND COMPLEXED WITH D(UP), REVEALS THE BASIS FOR ITS URIDINE SELECTIVITY. J.MOL.BIOL. V. 285 205 1999
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UM3 A:301;
B:302;
Valid;
Valid;
none;
none;
submit data
308.182 C9 H13 N2 O8 P C1[C@...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2RNF 2.4 Å EC: 3.1.27.- X-RAY CRYSTAL STRUCTURE OF HUMAN RIBONUCLEASE 4 IN COMPLEX WITH D(UP) HOMO SAPIENS RIBONUCLEASE HYDROLASE PHOSPHODIESTERASE
Ref.: THE THREE-DIMENSIONAL STRUCTURE OF HUMAN RNASE 4, UNLIGANDED AND COMPLEXED WITH D(UP), REVEALS THE BASIS FOR ITS URIDINE SELECTIVITY. J.MOL.BIOL. V. 285 205 1999
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2RNF - UM3 C9 H13 N2 O8 P C1[C@@H]([....
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 5ARK - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 2RNF - UM3 C9 H13 N2 O8 P C1[C@@H]([....
50% Homology Family (77)
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 5OGH - C3P C9 H14 N3 O8 P C1=CN(C(=O....
56 5NA9 - QPT C6 H12 N2 O4 Pt C1CC2(C1)C....
57 1F0V - DC DG n/a n/a
58 2W5L Ki = 63 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
59 1RUV - UVC C9 H12 N2 O9 V C1=CN(C(=O....
60 1Z6S Ki = 63 uM AMP C10 H14 N5 O7 P c1nc(c2c(n....
61 4G90 Ki = 30.8 uM 0G0 C12 H14 F N5 O6 c1c(nnn1[C....
62 6F60 - DVW C27 H31 N7 O5 Pt CC1=CC=C2C....
63 2W5G Ki = 0.86 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
64 3D8Z Ki = 423 uM TXS C14 H21 N3 O4 CC1=CN(C(=....
65 5JLG - RU Ru [Ru+3]
66 11BA - UPA C19 H24 N7 O12 P c1nc(c2c(n....
67 1TQ9 - CPA C19 H25 N8 O9 P c1nc(c2c(n....
68 3DJO Ki = 40.8 uM U2P C9 H13 N2 O9 P C1=CN(C(=O....
69 1N3Z - U3P C9 H13 N2 O9 P C1=CN(C(=O....
70 3DJV Ki = 27.9 uM C3P C9 H14 N3 O8 P C1=CN(C(=O....
71 1R5C - CPA C19 H25 N8 O9 P c1nc(c2c(n....
72 3DJQ Ki = 1046.4 uM UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
73 3DJP Ki = 63.2 uM UA3 C9 H13 N2 O9 P C1=CN(C(=O....
74 3DJX Ki = 1557 uM C5P C9 H14 N3 O8 P C1=CN(C(=O....
75 11BG - U2G C19 H24 N7 O13 P c1nc2c(n1[....
76 5ARK - UMP C9 H13 N2 O8 P C1[C@@H]([....
77 2RNF - UM3 C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UM3; Similar ligands found: 30
No: Ligand ECFP6 Tc MDL keys Tc
1 UM3 1 1
2 DUR 0.606557 0.838235
3 DU 0.57971 0.955224
4 UMP 0.57971 0.955224
5 T3P 0.573529 0.955882
6 DUD 0.540541 0.941176
7 UC5 0.52 0.927536
8 DU DU DU DU BRU DU DU 0.515789 0.851351
9 DUT 0.512821 0.941176
10 DUS 0.507042 0.815789
11 DUN 0.506494 0.914286
12 DUP 0.506329 0.914286
13 UA3 0.492958 0.939394
14 U2P 0.492958 0.897059
15 U3P 0.492958 0.939394
16 UMF 0.486111 0.884058
17 DDU 0.476923 0.73913
18 139 0.475728 0.810127
19 3PD UM3 0.447619 0.8
20 DU4 0.440476 0.723684
21 DU3 0.433735 0.767123
22 THP 0.43038 0.927536
23 URI 0.426471 0.782609
24 DUA 0.416667 0.77027
25 PUA 0.415929 0.820513
26 DU DU DU DU BRU DG DU 0.411765 0.752941
27 DUX 0.409639 0.767123
28 CJB 0.408451 0.742857
29 U 0.407895 0.897059
30 U5P 0.407895 0.897059
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2RNF; Ligand: UM3; Similar sites found with APoc: 53
This union binding pocket(no: 1) in the query (biounit: 2rnf.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 5U8U FAD None
2 1F5V FMN None
3 4USI ATP None
4 5J6C FMN None
5 1VE3 SAM None
6 3LAD FAD 1.66667
7 1BKJ FMN 1.66667
8 1QAN SAH 1.66667
9 5J62 FMN 2.5
10 6ALW BMJ 2.5
11 1O9J NAD 2.5
12 4A8H PUW 2.5
13 3NCQ ATP 2.52101
14 3TA2 AKG 2.54237
15 3TA2 ATP 2.54237
16 5XDT MB3 2.92208
17 4M52 FAD 3.33333
18 2A8X FAD 3.33333
19 3S1S SAH 3.33333
20 4H8N NDP 3.33333
21 3RNM FAD 4.16667
22 3KL3 GCU 4.16667
23 5WS9 AMP 5
24 4FK7 P34 5
25 5GZ6 7C3 5
26 5GZ6 NDP 5
27 2Q2V NAD 5
28 1DUV PSQ 5
29 1H82 GZZ 5.83333
30 3N2S FMN 5.83333
31 4POW OP1 5.83333
32 1UU6 BGC BGC BGC BGC 5.83333
33 5G1N PAL 5.83333
34 4L9Z OXL 6.66667
35 4L9Z COA 6.66667
36 2WBV SIA 6.66667
37 2QE0 NAP 6.66667
38 5HDJ FMN 6.66667
39 1DKU AP2 7.5
40 4XSH NAI 7.5
41 4RFM 3P6 7.5
42 1QFY NAP 7.5
43 1QFY FAD 7.5
44 3O9L LPN 7.5
45 2Z6J FMN 9.16667
46 5TCI 79V 9.16667
47 6F6J SIN 10
48 1I0S NAP 10
49 3ENG CBI 10.8333
50 4M26 ZZU 15.8333
51 4M26 SIN 15.8333
52 1JG3 ADN 23.3333
53 2BZZ AP5 41.6667
Pocket No.: 2; Query (leader) PDB : 2RNF; Ligand: UM3; Similar sites found with APoc: 16
This union binding pocket(no: 2) in the query (biounit: 2rnf.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1SS4 GSH None
2 5FUI APY None
3 5CFT APC 1.66667
4 5ANU 58T 3.33333
5 2F5Z FAD 4.16667
6 5BO9 CSF 5
7 5BO9 SIA GAL NGS 5
8 3WXM GTP 5.05319
9 1V59 FAD 5.83333
10 5Z2L NDP 6.66667
11 3QFA FAD 7.5
12 6F6J CUW 10
13 4B7X NAP 10
14 6EXF LYS 11.6667
15 1U2Z SAH 14.1667
16 1PTR PRB 22
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