Receptor
PDB id Resolution Class Description Source Keywords
1E4X 1.9 Å NON-ENZYME: IMMUNE CROSSREACTIVE BINDING OF A CIRCULARIZED PEPTIDE TO AN ANTI-TGFALPHA ANTIBODY FAB-FRAGMENT MUS MUSCULUS IMMUNE SYSTEM COMPLEX (ANTIBODY/ANTIGEN) CROSS-REACTIVITY PROTEIN-PEPTIDE RECOGNITION
Ref.: CROSS-REACTIVE BINDING OF CYCLIC PEPTIDES TO AN ANTI-TGF ALPHA ANTIBODY FAB FRAGMENT: AN X-RAY STRUCTURAL AND THERMODYNAMIC ANALYSIS J.MOL.BIOL. V. 314 293 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
VAL VAL SER HIS PHE ASN ASP P:1;
Q:1;
Valid;
Valid;
none;
none;
Kd = 25 nM
815.862 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1E4X 1.9 Å NON-ENZYME: IMMUNE CROSSREACTIVE BINDING OF A CIRCULARIZED PEPTIDE TO AN ANTI-TGFALPHA ANTIBODY FAB-FRAGMENT MUS MUSCULUS IMMUNE SYSTEM COMPLEX (ANTIBODY/ANTIGEN) CROSS-REACTIVITY PROTEIN-PEPTIDE RECOGNITION
Ref.: CROSS-REACTIVE BINDING OF CYCLIC PEPTIDES TO AN ANTI-TGF ALPHA ANTIBODY FAB FRAGMENT: AN X-RAY STRUCTURAL AND THERMODYNAMIC ANALYSIS J.MOL.BIOL. V. 314 293 2001
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP 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 1068 families.
1 5DS8 - GLY 5CT GLY ALA n/a n/a
2 1FE8 - NAG C8 H15 N O6 CC(=O)N[C@....
3 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP n/a n/a
4 4MA8 - Z80 C17 H19 Cl N2 S CN(C)CCCN1....
5 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3U7Y - FLC C6 H5 O7 C(C(=O)[O-....
2 1NC4 - DOF C23 H33 N5 O10 c1cc(ccc1C....
3 5DS8 - GLY 5CT GLY ALA n/a n/a
4 5DRN - 5CT C10 H23 N3 O3 C(CCNC[C@H....
5 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
6 1QKZ - ALA ASN GLY GLY ALA SER GLY GLN VAL LYS n/a n/a
7 1NC2 - DOE C27 H41 N5 O10 S c1cc(ccc1C....
8 2HVK - TBA C16 H36 N CCCC[N+](C....
9 5DUB - GLY 5GG GLY ALA n/a n/a
10 5MES ic50 = 0.045 uM 7LT C44 H49 Cl2 N5 O4 CN1CCCN[C@....
11 1FE8 - NAG C8 H15 N O6 CC(=O)N[C@....
12 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
13 5T85 - 44G C18 H35 O10 P CCCCCC(=O)....
14 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP n/a n/a
15 4MA7 - P2Z C17 H20 N2 S CN(C)CCCN1....
16 4MA8 - Z80 C17 H19 Cl N2 S CN(C)CCCN1....
17 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
18 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
19 2DWE - TBA C16 H36 N CCCC[N+](C....
20 3PGF - GLC GLC n/a n/a
21 1MJJ Kd = 1.83 nM HAL C23 H29 N2 O7 P c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VAL VAL SER HIS PHE ASN ASP; Similar ligands found: 87
No: Ligand ECFP6 Tc MDL keys Tc
1 VAL VAL SER HIS PHE ASN ASP 1 1
2 ALA LYS PHE ARG HIS ASP 0.563025 0.746032
3 ASP ALA GLU PHE ARG HIS ASP 0.558333 0.758065
4 SER HIS PHE ASN GLU TYR GLU 0.515152 0.85
5 ACE PHE HIS THR ABA NH2 0.508772 0.807018
6 GLU THR LEU GLU ASP SER VAL PHE 0.490566 0.777778
7 ALA SER ASN GLU HIS MET GLU THR MET 0.484615 0.822581
8 ILE ASN PHE ASP PHE ASN THR ILE 0.483051 0.741379
9 ACE PHE HIS THR GLY NH2 0.482759 0.859649
10 TYR PRO ASN VAL ASN ILE HIS ASN PHE 0.48 0.71831
11 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.473684 0.676056
12 SER LEU PHE ASN THR VAL ALA THR LEU 0.472441 0.785714
13 VAL GLN GLN GLU SER SER PHE VAL MET 0.472 0.721311
14 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.471014 0.690141
15 SER LEU PHE ASN THR ILE ALA VAL LEU 0.465649 0.789474
16 ASP PHE SER ILE 0.463636 0.732143
17 SER HIS VAL ALA VAL GLU ASN ALA LEU 0.462121 0.928571
18 ACE PHE HIS ALA ALA NH2 0.460177 0.745455
19 ACE THR VAL ALC HSO 0.458333 0.854545
20 PHE SER HIS PRO GLN ASN THR 0.457746 0.787879
21 ILE LEU ALA LYS PHE LEU HIS THR LEU 0.457143 0.803279
22 ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR 0.456954 0.732394
23 VAL ASN ASP ILE PHE GLU ALA ILE 0.450382 0.719298
24 DVA DPR GLY DSN DGN DHI DTY DAS DSN 0.450331 0.794118
25 ACE SER ALA VAL ALC HSO 0.448819 0.909091
26 GLU GLU ASN LEU LEU ASP PHE VAL ARG PHE 0.446043 0.703125
27 VAL LEU HIS ASP ASP LEU LEU GLU ALA 0.442623 0.803571
28 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 0.439189 0.791045
29 LYS SER HIS GLN GLU 0.439024 0.827586
30 SER VAL TYR ASP PHE PHE VAL TRP LEU 0.438849 0.833333
31 THR LYS ASN TYR LYS GLN PHE SER VAL 0.438462 0.758065
32 ALA VAL TYR ASN PHE ALA THR MET 0.437037 0.6875
33 GLY ALA PHE THR PHE ASN GLU ASP PHE 0.436508 0.736842
34 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.436242 0.689189
35 GLY ASN PHE LEU GLN SER ARG 0.43609 0.71875
36 ILE LEU ALA LYS PHE LEU HIS GLU LEU 0.435714 0.766667
37 ARG GLN VAL ASN PHE LEU GLY LYS ILE ASN 0.435484 0.684211
38 ALA THR ARG ASN PHE SER GLY 0.435115 0.6875
39 LYS PRO HIS SER ASP 0.435115 0.738462
40 MET PHE SER ILE ASP ASN ILE LEU ALA 0.434783 0.754098
41 LYS ALA VAL PHE ASN PHE ALA THR MET 0.433824 0.676923
42 GLY ASN TYR SER PHE TYR ALA LEU 0.433071 0.754098
43 CYS VAL ASN GLY SER CYS PHE THR VAL 0.432836 0.775862
44 TYR GLN GLU SER THR ASP PHE THR PHE LEU 0.432203 0.701754
45 GLU LYS VAL HIS VAL GLN 0.432 0.775862
46 GLY VAL TYR ASP GLY ARG GLU HIS THR VAL 0.430464 0.80303
47 PHE ASN GLU LEU SER HIS LEU 0.429752 0.892857
48 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU 0.426471 0.758621
49 ASP HIS ASP ALA HIS ALA 0.426087 0.833333
50 GLY ALA ARG ALA HIS SER SER 0.425197 0.809524
51 ACE SER HIS VAL ALA VAL GLU ASN ALA LEU 0.42446 0.912281
52 DHI PRO PHE HIS LEU LEU VAL TYR 0.424051 0.657143
53 GLY SER SER HIS HIS HIS HIS HIS 0.423423 0.875
54 SER SER LEU GLU ASN PHE ALA ALA TYR VAL 0.422535 0.783333
55 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.421429 0.7
56 GLY SER HIS LEU GLU VAL GLN GLY TYR TRP 0.419753 0.828125
57 SER HIS LYS ILE ASP ASN LEU ASP 0.41844 0.866667
58 ASP ARG VAL TYR ILE HIS PRO PHE 0.418182 0.657895
59 HIS ILE PHE SER 0.418033 0.732143
60 ILE LEU GLY LYS PHE LEU HIS ARG LEU 0.417808 0.727273
61 PCA PHE ARG HIS ASP SER 0.417266 0.71875
62 HIS VAL ALA VAL GLU ASN ALA LEU 0.416667 0.821429
63 LEU GLY TYR GLY PHE VAL ASN TYR ILE 0.416058 0.709677
64 LEU LEU TYR GLY PHE VAL ASN TYR VAL 0.413043 0.721311
65 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.413043 0.75
66 PHE SER GLN HIS LYS THR SER TPO ILE 0.412903 0.753623
67 LYS ALA VAL TYR ASN PHE ALA THR MET 0.412587 0.671642
68 THR PHE LYS LYS THR ASN 0.409836 0.728814
69 LYS VAL LEU PHE LEU ASP GLY 0.409449 0.633333
70 SER LEU PHE ASN THR VAL ALA THR LEU TYR 0.408451 0.762712
71 LEU LEU TYR GLY PHE VAL ASN TYR ILE 0.408451 0.709677
72 PCA PHE ARG HIS ASP SER GLY TYR GLU VAL 0.408284 0.80597
73 ALA HIS HIS 0.407767 0.759259
74 GLN VAL ASN PHE LEU GLY LYS 0.407407 0.7
75 PHE LEU PRO SER ASP PHE PHE PRO SER VAL 0.407143 0.746269
76 SER PHE PHE GLU ASP ASN PHE VAL PRO GLU 0.407143 0.772727
77 VAL TYR ILE HIS PRO PHE 0.406667 0.633803
78 GLU LEU ASP HIS TRP ALA SER 0.405594 0.912281
79 SER ILE ILE ASN PHE GLU LYS LEU 0.404412 0.75
80 THR GLU ASN LEU TYR PHE GLN SER GLY THR 0.40411 0.746032
81 GLU THR VAL ARG PHE GLN SER ASP 0.402778 0.714286
82 MET ASP TRP ASN MET HIS ALA ALA 0.402778 0.790323
83 ILE ASP TRP PHE ASP GLY LYS ASP 0.402778 0.714286
84 SER ASN TRP SER HIS PRO GLN PHE GLU LYS 0.402439 0.746269
85 THR ASN GLU PHE TYR ALA 0.401575 0.728814
86 ACE PHE HIS THR ALA NH2 0.4 0.821429
87 PHE GLU ASP ASN PHE VAL PRO 0.4 0.727273
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1E4X; Ligand: VAL VAL SER HIS PHE ASN ASP; Similar sites found: 35
This union binding pocket(no: 1) in the query (biounit: 1e4x.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SS4 CIT 0.005977 0.4942 None
2 3R51 MMA 0.02388 0.40636 1.875
3 3S9K CIT 0.001446 0.50318 2.54237
4 3F81 STT 0.00472 0.44106 2.73224
5 3FW3 GLC 0.01017 0.4551 3.22581
6 1Z42 HBA 0.004541 0.46839 3.68664
7 9LDB OXM 0.01614 0.42227 3.73832
8 3UR0 SVR 0.01726 0.40431 3.73832
9 1JAC AMG 0.03006 0.40826 3.7594
10 3QDW A2G 0.009315 0.42655 4.8951
11 3QDY A2G GAL 0.0115 0.41504 4.8951
12 3QDT A2G GAL 0.01785 0.40601 4.8951
13 4B16 NAG 0.01685 0.4213 5.14019
14 3IHB TRS 0.000006643 0.6667 5.52995
15 1WRA PC 0.003783 0.43057 5.52995
16 2YIV YIV 0.006209 0.42766 5.60748
17 1BTN I3P 0.001842 0.48854 5.66038
18 1HFA PIO 0.00009036 0.58592 5.99078
19 1JGS SAL 0.02312 0.42228 6.52174
20 2JFV FLC 0.008394 0.40889 6.54206
21 1Y1A GSH 0.00176 0.49046 6.55738
22 1KC7 PPR 0.01492 0.40357 7.37327
23 2W3L DRO 0.01109 0.42281 8.29493
24 2Q8H TF4 0.01595 0.41503 8.29493
25 1V7R CIT 0.008741 0.43601 9.13978
26 1WHT BZS 0.001684 0.43926 9.15033
27 4JCA CIT 0.01649 0.42179 9.58084
28 3E6J DR2 0.01662 0.41777 9.67742
29 1JN2 SFP 0.03451 0.42894 10.1382
30 1PEA ACM 0.006462 0.42685 10.7477
31 2YD6 FLC 0.000842 0.52534 15.0943
32 1NU4 MLA 0.007169 0.44985 19.5876
33 2V5E SCR 0.04081 0.40133 20.7921
34 2X2T GAL NGA 0.01107 0.42285 22.2222
35 4WBD ADP 0.01265 0.40683 30.3738
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