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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;
Atoms found LESS than expected: % Diff = 0;
Kd = 12.88 uM
433.577 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 36 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 6 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 (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 5TDC Kd = 12.88 uM NMM ILE PHE SER n/a n/a
2 3NIL - ARG ASP ALA ALA n/a n/a
3 3NIJ - HIS ILE ALA ALA n/a n/a
4 3NIH - ARG ILE ALA ALA ALA n/a n/a
5 3NII - LYS ILE ALA ALA n/a n/a
6 3NIM Kd = 17.7 uM ARG ARG ALA ALA n/a n/a
7 3NIK Kd = 358.8 uM ARG GLU ALA ALA n/a n/a
8 3NIN - ARG LEU GLY GLU SER n/a n/a
9 5TDB Kd = 1.45 uM DA2 ILE PHE SER n/a n/a
10 3NY3 Kd = 19 uM ARG ILE PHE SER n/a n/a
11 5TDA - ARG LEU TRP SER n/a n/a
12 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: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 NMM ILE PHE SER 1 1
2 ARG ILE PHE SER 0.595745 0.882353
3 ARG ILE ALA ALA ALA 0.481928 0.87234
4 ALA VAL GLY ILE GLY ALA VAL PHE 0.480392 0.77551
5 ALA VAL GLY ILE GLY ALA VAL PHE LEU 0.480392 0.77551
6 ALA ALA PHE 0.45679 0.617021
7 LYS LEU LEU PHE 0.456522 0.77551
8 ARG ARG LEU ILE PHE NH2 0.443396 0.918367
9 ARG ABA PHE ILE PHE ALA ASN ILE 0.423729 0.818182
10 HIS ILE PHE SER 0.413462 0.625
11 ARG ABA VAL ILE PHE ALA ASN ILE 0.413223 0.833333
12 LYS ILE ALA ALA 0.404762 0.729167
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 with APoc: 86
This union binding pocket(no: 1) in the query (biounit: 5tdc.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 2O4N TPV None
2 4P3H 25G None
3 2FXD DR7 None
4 6FIV 3TL None
5 2P3B 3TL None
6 4Q5M ROC None
7 2VZZ SCA None
8 4W6Z 8ID None
9 2Z9C DTC None
10 3MWS 017 None
11 3FSM 2NC None
12 4R57 ACO None
13 5T2Z 017 None
14 3S43 478 None
15 2RIF AMP None
16 4DPL NAP 2.63158
17 3NUB UD0 2.63158
18 5NV9 SLB 2.63158
19 5K8B PDG 2.63158
20 1VG8 GNP 2.63158
21 1RM0 D6P 3.94737
22 1RM0 NAI 3.94737
23 3E5H GNP 3.94737
24 2GZ3 NAP 3.94737
25 1C1X NAD 3.94737
26 3W9F I3P 3.94737
27 6G5J EM8 4.24242
28 1P3D UMA 5.26316
29 5W71 PLP 5.26316
30 5W71 9YM 5.26316
31 1H74 ILE 5.26316
32 5BU2 ADP 6.57895
33 4GE6 B26 6.57895
34 1RE8 BD2 6.57895
35 2B8W ALF 5GP 6.57895
36 3UR0 SVR 6.57895
37 1DJL NAP 6.57895
38 3ZOK GLY 7.89474
39 4HSE ADP 7.89474
40 3T3C 017 7.89474
41 1FMB HYB 7.89474
42 2BO4 FLC 7.89474
43 5C2H 4PX 9.21053
44 5HMY LNY 9.21053
45 2H04 4UN 9.21053
46 1T9D P25 10.5263
47 1T9D FAD 10.5263
48 1T9D 1MM 10.5263
49 1T9D PYD 10.5263
50 6DEN TP9 10.5263
51 6DEN G8A 10.5263
52 6DEN FAD 10.5263
53 1ELU PDA 10.5263
54 1ELU CSS 10.5263
55 3VYW SAM 10.5263
56 4C2V YJA 10.5263
57 1IDA 0PO 10.5263
58 2CNE DFJ 10.5263
59 3QVV A3P 10.5263
60 5EYK 5U5 10.5263
61 2QV7 ADP 11.8421
62 3DST GRG 11.8421
63 5ITZ GDP 11.8421
64 5EYP GDP 11.8421
65 5EIB GTP 11.8421
66 3SFX FII 11.8421
67 3SFX JAN 11.8421
68 4LNU GDP 11.8421
69 3LN0 52B 13.1579
70 4Z3X 4KX 13.1579
71 3SM2 478 13.1579
72 4Z3X MTE 13.1579
73 1SIV PSI 13.1579
74 3SUD SUE 13.1579
75 2R2L FPP 13.1579
76 2R2L PB9 13.1579
77 2PA4 UPG 14.4737
78 1XSE NDP 14.4737
79 2FAH GDP 15.7895
80 1NHX FTB 18.4211
81 1NHX PEP 18.4211
82 3GFB NAD 18.4211
83 4I4B 1CV 19.7368
84 4LX0 BEF GDP 21.0526
85 5WS9 AMP 25
86 3CRZ NAP 27.6316
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