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Receptor
PDB id Resolution Class Description Source Keywords
2DJH 1.9 Å EC: 3.1.-.- CRYSTAL STRUCTURE OF THE CARBOXY-TERMINAL RIBONUCLEASE DOMAIN OF COLICIN E5 ESCHERICHIA COLI ALPHA/BETA PROTEIN HYDROLASE
Ref.: STRUCTURAL BASIS FOR SEQUENCE-DEPENDENT RECOGNITION OF COLICIN E5 TRNASE BY MIMICKING THE MRNA-TRNA INTERACTION NUCLEIC ACIDS RES. V. 34 6074 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PD UM3 A:117;
Valid;
none;
submit data
634.368 n/a P(=O)...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2DJH 1.9 Å EC: 3.1.-.- CRYSTAL STRUCTURE OF THE CARBOXY-TERMINAL RIBONUCLEASE DOMAIN OF COLICIN E5 ESCHERICHIA COLI ALPHA/BETA PROTEIN HYDROLASE
Ref.: STRUCTURAL BASIS FOR SEQUENCE-DEPENDENT RECOGNITION OF COLICIN E5 TRNASE BY MIMICKING THE MRNA-TRNA INTERACTION NUCLEIC ACIDS RES. V. 34 6074 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 2DJH - 3PD UM3 n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 2DJH - 3PD UM3 n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 2DJH - 3PD UM3 n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3PD UM3; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 3PD UM3 1 1
2 DU DU DU DU BRU DG DU 0.798319 0.940476
3 DA DU DG DA 0.758929 0.939024
4 DG DG 0.685185 0.926829
5 DC DG 0.612903 0.975309
6 DG DA DC DG 0.609929 0.963415
7 DG DC 0.571429 0.939024
8 DC DG DA DC 0.541667 0.939024
9 DU DU DU DU BRU DA DU 0.527397 0.83908
10 DA DC DG DA 0.526316 0.927711
11 DC DG DT DA 0.509434 0.917647
12 CGP 0.507576 0.951219
13 DT DA DC DG 0.503145 0.917647
14 G U 0.5 0.938272
15 DU DU DU DU BRU DU DU 0.496063 0.755814
16 DGI 0.474138 0.86747
17 DGP 0.473214 0.878049
18 DG 0.473214 0.878049
19 DA DT DA DA 0.465278 0.858824
20 UM3 0.447619 0.8
21 DGT 0.446281 0.86747
22 U2G 0.437956 0.903614
23 A G U 0.437909 0.926829
24 DT MA7 DT 0.433333 0.860465
25 G U34 0.42446 0.926829
26 A G U U 0.424051 0.926829
27 G C 0.41844 0.938272
28 139 0.414286 0.869048
29 DC DC DT DG 0.412214 0.817073
30 PUA 0.410959 0.879518
31 G G G RPC 0.408451 0.9375
32 ALF 5GP 0.403226 0.816092
33 UCG 0.4 0.902439
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2DJH; Ligand: 3PD UM3; Similar sites found with APoc: 48
This union binding pocket(no: 1) in the query (biounit: 2djh.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 6FTB M0E None
2 4PYA 2X3 None
3 1SQL GUN None
4 6MJ7 ARG None
5 4K55 H6P None
6 2XOC ADE 1.73913
7 3ORQ ADP 2.6087
8 2D24 XYS XYS 3.47826
9 1UPR 4IP 3.47826
10 3UG4 AHR 4.34783
11 5H4S RAM 4.34783
12 4LO2 GAL BGC 4.34783
13 4ZGR NGA GAL 4.34783
14 4OWK NGA 4.34783
15 1MAI I3P 4.34783
16 4K6B GLU 4.34783
17 2C3W GLC GLC GLC GLC 4.90196
18 2ZQO NGA 5.21739
19 4NFE BEN 6.08696
20 3FSY SCA 6.08696
21 4GDX GLU 6.08696
22 1D4D SIN 6.95652
23 4I4S LAT 7.82609
24 3A23 GAL 7.82609
25 6C90 ADP 7.82609
26 5L4R CPT 9.56522
27 3THR C2F 9.56522
28 1JG3 VAL TYR PRO IAS HIS ALA 9.56522
29 3BP1 GUN 9.56522
30 5GQX GLC GLC GLC GLC 10.4348
31 4NZ6 DLY 10.4348
32 4LJ9 ACP 10.4348
33 2Y9G LBT 11.3043
34 2Y9G LAT 11.3043
35 2H88 TEO 12.1429
36 1KNM LAT 12.1739
37 3ZGE ASP 12.1739
38 4JDR FAD 12.1739
39 1ZX5 LFR 12.1739
40 3EF0 ALF 13.913
41 3BMO AX4 14.7826
42 4CS9 AMP 15.6522
43 2UYQ SAM 15.6522
44 4JLS 3ZE 17.3913
45 3IWD M2T 19.1176
46 1PVC ILE SER GLU VAL 20
47 4JGT PYR 21.7391
48 3A75 GLU 23.4783
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