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Receptor
PDB id Resolution Class Description Source Keywords
5ARK 2.28 Å EC: 3.1.27.- CRYSTAL STRUCTURE OF PORCINE RNASE 4 IN COMPLEX WITH DUMP SUS SCROFA RIBONUCLEASE 4 HYDROLASE RNA DEGRADATION
Ref.: STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY IN PORCIN 4. FEBS J. V. 283 912 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UMP B:1120;
C:1120;
A:1120;
D:1120;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
308.182 C9 H13 N2 O8 P C1[C@...
PO4 A:1121;
B:1121;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ARK 2.28 Å EC: 3.1.27.- CRYSTAL STRUCTURE OF PORCINE RNASE 4 IN COMPLEX WITH DUMP SUS SCROFA RIBONUCLEASE 4 HYDROLASE RNA DEGRADATION
Ref.: STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY IN PORCIN 4. FEBS J. V. 283 912 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5ARK - UMP 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: UMP; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 DU 1 1
2 UMP 1 1
3 DUD 0.8 0.985075
4 UC5 0.772727 0.970588
5 DUT 0.753623 0.985075
6 DUN 0.75 0.956522
7 DUP 0.742857 0.956522
8 DUS 0.692308 0.853333
9 DUR 0.683333 0.852941
10 DDN 0.632353 1
11 UFP 0.591549 0.929577
12 TMP 0.583333 0.956522
13 BRU 0.583333 0.929577
14 5HU 0.583333 0.942857
15 UM3 0.57971 0.955224
16 5IU 0.575342 0.929577
17 DC 0.561644 0.928571
18 DCM 0.561644 0.928571
19 BVP 0.531646 0.942857
20 DU DU DU DU BRU DU DU 0.53125 0.864865
21 U 0.527778 0.911765
22 U5P 0.527778 0.911765
23 DDU 0.523077 0.753623
24 UMC 0.520548 0.941176
25 QBT 0.493333 0.927536
26 DUA 0.487805 0.783784
27 DU3 0.487805 0.780822
28 DU4 0.47619 0.76
29 TYD 0.469136 0.942857
30 YYY 0.451219 0.915493
31 UDP 0.45 0.898551
32 TTP 0.447059 0.942857
33 8OG 0.435294 0.835443
34 U3P 0.434211 0.897059
35 UA3 0.434211 0.897059
36 U2P 0.434211 0.884058
37 UTP 0.433735 0.898551
38 44P 0.43038 0.914286
39 DCP 0.430233 0.915493
40 2KH 0.411765 0.873239
41 DUX 0.411765 0.756757
42 UMF 0.410256 0.84507
43 139 0.409091 0.8
44 UPU 0.409091 0.871429
45 URI 0.408451 0.771429
46 TBD 0.406977 0.90411
47 DU DU DU DU BRU DA DU 0.40625 0.771084
48 PUA 0.405172 0.833333
49 UNP 0.402299 0.873239
50 UDX 0.4 0.873239
51 PUP 0.4 0.955882
52 UAD 0.4 0.873239
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ARK; Ligand: UMP; Similar sites found with APoc: 25
This union binding pocket(no: 1) in the query (biounit: 5ark.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 3R7F CP None
2 3BNK FMN 1.49254
3 2A8X FAD 2.23881
4 4M52 FAD 2.23881
5 3A2Q ACA ACA 2.98507
6 5XDT MB3 3.57143
7 4B5P ACO 4.47761
8 4XT8 NAP 4.47761
9 5G1N PAL 5.22388
10 1U2Z SAH 5.97015
11 5WS9 AMP 5.97015
12 4L9Z COA 5.97015
13 4L9Z OXL 5.97015
14 2WBV SIA 6.71642
15 1QFY FAD 6.71642
16 1QFY NAP 6.71642
17 3KL3 GCU 6.71642
18 1H0H 2MD 7.46269
19 2NYA MGD 8.95522
20 6F6J CUW 10.4478
21 6F6J SIN 10.4478
22 3ML1 MGD 14.1791
23 1PTR PRB 16
24 1DKU AP2 17.1642
25 2BZZ AP5 37.3134
Pocket No.: 2; Query (leader) PDB : 5ARK; Ligand: UMP; Similar sites found with APoc: 19
This union binding pocket(no: 2) in the query (biounit: 5ark.bio4) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 3GXZ BMA MAN MAN MAN None
2 3JQM GTP None
3 3GXZ NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN None
4 2CYE COA None
5 2WKQ GTP 1.49254
6 4ZAD 4LU 2.23881
7 6ECW SAH 2.98507
8 1BKJ FMN 2.98507
9 4GAH 0ET 4.47761
10 6BOX SAH 4.47761
11 5VFC 9BA 5.22388
12 5V22 SAH 5.22388
13 1NY5 ADP 5.97015
14 4HDO GNP 6.71642
15 2Z6J FMN 8.20895
16 4ZAC 4LU 8.95522
17 5A65 TPP 13.4328
18 6CEN SAM 15.6716
19 5JLB SAH 17.9104
Pocket No.: 3; Query (leader) PDB : 5ARK; Ligand: UMP; Similar sites found with APoc: 7
This union binding pocket(no: 3) in the query (biounit: 5ark.bio3) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1KAO GDP None
2 4CP8 MLI 2.98507
3 3THR C2F 2.98507
4 3WOL VAL TYR 3.73134
5 6HTO MET 6.71642
6 6HTO 5AD 6.71642
7 3F5A SIA GAL NAG 10.4478
Pocket No.: 4; Query (leader) PDB : 5ARK; Ligand: UMP; Similar sites found with APoc: 6
This union binding pocket(no: 4) in the query (biounit: 5ark.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1ADO 13P None
2 4GCZ ADP 2.98507
3 5TCI 79V 3.73134
4 5GVL GI8 4.47761
5 5GVL PLG 4.47761
6 2ZAT NAP 5.22388
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