Receptor
PDB id Resolution Class Description Source Keywords
5TDC 1.61 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF THE HUMAN UBR-BOX DOMAIN FROM UBR1 IN C WITH MONOMETHYLATED ARGININE PEPTIDE. HOMO SAPIENS UBR-BOX N-END RULE N-DEGRON MONOMETHYLATED ARGININE LIGA
Ref.: BOUND WATERS MEDIATE BINDING OF DIVERSE SUBSTRATES UBIQUITIN LIGASE. STRUCTURE V. 25 719 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN C:201;
A:203;
A:202;
C:203;
C:202;
A:201;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
NMM ILE PHE SER D:1;
B:1;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.053;
Atoms found LESS than expected: % Diff = 0.184;
Kd = 12.88 uM
506.672 n/a O=C(N...
SO4 C:204;
A:204;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TDC 1.61 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF THE HUMAN UBR-BOX DOMAIN FROM UBR1 IN C WITH MONOMETHYLATED ARGININE PEPTIDE. HOMO SAPIENS UBR-BOX N-END RULE N-DEGRON MONOMETHYLATED ARGININE LIGA
Ref.: BOUND WATERS MEDIATE BINDING OF DIVERSE SUBSTRATES UBIQUITIN LIGASE. STRUCTURE V. 25 719 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 34 families.
1 5TDC Kd = 12.88 uM NMM ILE PHE SER n/a n/a
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 5TDC Kd = 12.88 uM NMM ILE PHE SER n/a n/a
2 5TDB Kd = 1.45 uM DA2 ILE PHE SER n/a n/a
3 3NY3 Kd = 19 uM ARG ILE PHE SER n/a n/a
4 5TDA - ARG LEU TRP SER n/a n/a
5 5TDD Kd = 34 uM HIS ILE PHE SER n/a n/a
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 5TDC Kd = 12.88 uM NMM ILE PHE SER n/a n/a
2 3NIJ - HIS ILE ALA ALA n/a n/a
3 3NII - LYS ILE ALA ALA n/a n/a
4 3NIM Kd = 17.7 uM ARG ARG ALA ALA n/a n/a
5 3NIK Kd = 358.8 uM ARG GLU ALA ALA n/a n/a
6 3NIN - ARG LEU GLY GLU SER n/a n/a
7 5TDB Kd = 1.45 uM DA2 ILE PHE SER n/a n/a
8 3NY3 Kd = 19 uM ARG ILE PHE SER n/a n/a
9 5TDA - ARG LEU TRP SER n/a n/a
10 5TDD Kd = 34 uM HIS ILE PHE SER n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NMM ILE PHE SER; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 NMM ILE PHE SER 1 1
2 ARG ILE PHE SER 0.468468 0.901961
3 THR PHE ALY SER ILE MET LYS 0.415254 0.732143
4 ALA PHE THR 0.410526 0.64
5 GLU ARG GLU SEP GLU PHE ASP ILE GLU ASP 0.407143 0.714286
6 VAL ALA PHE ARG SER 0.405172 0.846154
7 ARG PRO GLY ASN PHE PHE GLN ASN ARG PRO 0.403509 0.62069
8 ARG ABA PHE ILE PHE ALA ASN ILE 0.401575 0.803571
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TDC; Ligand: NMM ILE PHE SER; Similar sites found: 65
This union binding pocket(no: 1) in the query (biounit: 5tdc.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2O4N TPV 0.009406 0.43512 None
2 4P3H 25G 0.008058 0.42869 None
3 2FXD DR7 0.01549 0.42727 None
4 2P3B 3TL 0.03155 0.41867 None
5 4Q5M ROC 0.02339 0.41769 None
6 2VZZ SCA 0.03308 0.41188 None
7 3MWS 017 0.04399 0.40592 None
8 3FSM 2NC 0.04905 0.40566 None
9 3NWQ 2NC 0.04754 0.40211 None
10 5T2Z 017 0.04797 0.40188 None
11 3S43 478 0.04263 0.40149 None
12 2RIF AMP 0.02224 0.40016 None
13 5K8B PDG 0.02484 0.40343 2.63158
14 1VG8 GNP 0.04464 0.40081 2.63158
15 4GQL R47 0.01686 0.43335 3.94737
16 3E5H GNP 0.01438 0.42608 3.94737
17 1IMB LIP 0.01712 0.40013 3.94737
18 1P3D UMA 0.01832 0.42211 5.26316
19 5W71 PLP 0.009271 0.41777 5.26316
20 5W71 9YM 0.03141 0.41542 5.26316
21 1H74 ILE 0.04502 0.40318 5.26316
22 4GE6 B26 0.01313 0.42112 6.57895
23 1RE8 BD2 0.04323 0.41121 6.57895
24 2B8W ALF 5GP 0.02573 0.40898 6.57895
25 4HSE ADP 0.01258 0.41031 7.89474
26 3T3C 017 0.04726 0.40178 7.89474
27 2BO4 FLC 0.03401 0.40027 7.89474
28 5C2H 4PX 0.0276 0.4239 9.21053
29 5HMY LNY 0.03316 0.42006 9.21053
30 2H04 4UN 0.02258 0.40086 9.21053
31 1T9D P25 0.0381 0.44112 10.5263
32 1T9D PYD 0.0398 0.43965 10.5263
33 1T9D FAD 0.0398 0.43965 10.5263
34 1T9D 1MM 0.04049 0.43965 10.5263
35 1ELU PDA 0.01212 0.41648 10.5263
36 1ELU CSS 0.0169 0.41256 10.5263
37 3VYW SAM 0.01989 0.4113 10.5263
38 4C2V YJA 0.0353 0.40895 10.5263
39 1IDA 0PO 0.04554 0.4073 10.5263
40 5CPR SAM 0.03525 0.40699 10.5263
41 2CNE DFJ 0.04603 0.4061 10.5263
42 5EYK 5U5 0.04258 0.40159 10.5263
43 2QV7 ADP 0.003325 0.44263 11.8421
44 5ITZ GDP 0.01697 0.42146 11.8421
45 5EYP GDP 0.02313 0.41869 11.8421
46 3SFX JAN 0.03459 0.41098 11.8421
47 3SFX FII 0.03459 0.41098 11.8421
48 4LNU GDP 0.02561 0.40845 11.8421
49 3LN0 52B 0.01813 0.44212 13.1579
50 4Z3X 4KX 0.03078 0.43814 13.1579
51 3SM2 478 0.02144 0.42773 13.1579
52 4Z3X MTE 0.04741 0.42434 13.1579
53 1SIV PSI 0.04072 0.40709 13.1579
54 3SUD SUE 0.02893 0.40589 13.1579
55 2R2L FPP 0.04417 0.4056 13.1579
56 2R2L PB9 0.0469 0.4041 13.1579
57 2PA4 UPG 0.01877 0.42704 14.4737
58 1XSE NDP 0.04452 0.41596 14.4737
59 2FAH GDP 0.004988 0.43821 15.7895
60 1NHX PEP 0.01447 0.4404 18.4211
61 1NHX FTB 0.01499 0.4404 18.4211
62 3GFB NAD 0.03383 0.40655 18.4211
63 4I4B 1CV 0.03661 0.41085 19.7368
64 4LX0 BEF GDP 0.03528 0.40062 21.0526
65 3CRZ NAP 0.02192 0.42656 27.6316
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