Receptor
PDB id Resolution Class Description Source Keywords
5VNF 2.41 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF SEC23A/SEC24A/SEC22 COMPLEXED WITH A C- VV SORTING MOTIF HOMO SAPIENS COPII TRAFFICKING P24 ER RETENTION PROTEIN TRANSPORT
Ref.: ER RETENTION IS IMPOSED BY COPII PROTEIN SORTING AN ATTENUATED BY 4-PHENYLBUTYRATE. ELIFE V. 6 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:1101;
A:801;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
VAL THR SER VAL VAL D:7;
Valid;
Atoms found LESS than expected: % Diff = 0.114;
Kd = 14.2 uM
445.517 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VNF 2.41 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF SEC23A/SEC24A/SEC22 COMPLEXED WITH A C- VV SORTING MOTIF HOMO SAPIENS COPII TRAFFICKING P24 ER RETENTION PROTEIN TRANSPORT
Ref.: ER RETENTION IS IMPOSED BY COPII PROTEIN SORTING AN ATTENUATED BY 4-PHENYLBUTYRATE. ELIFE V. 6 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 5VNF Kd = 14.2 uM VAL THR SER VAL VAL n/a n/a
2 5VNL - CLT C10 H12 O2 c1ccc(cc1)....
3 5VNN - CLT C10 H12 O2 c1ccc(cc1)....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 5VNF Kd = 14.2 uM VAL THR SER VAL VAL n/a n/a
2 5VNL - CLT C10 H12 O2 c1ccc(cc1)....
3 5VNN - CLT C10 H12 O2 c1ccc(cc1)....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 141 families.
1 5VNF Kd = 14.2 uM VAL THR SER VAL VAL n/a n/a
2 5VNL - CLT C10 H12 O2 c1ccc(cc1)....
3 5VNN - CLT C10 H12 O2 c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VAL THR SER VAL VAL; Similar ligands found: 29
No: Ligand ECFP6 Tc MDL keys Tc
1 VAL THR SER VAL VAL 1 1
2 ASP GLU VAL THR SER THR THR SER SER SER 0.661538 0.948718
3 ALA ALA ALA ALA SER ALA ALA 0.642857 0.972973
4 ALA ALA SER ALA SER ALA 0.55 0.921053
5 PHE GLU ALA LYS LYS LEU VAL 0.528571 0.704545
6 SER PRO SER ILE 0.525424 0.923077
7 ALA SER VAL SER ALA 0.516129 0.947368
8 LYS GLN THR SER VAL 0.514286 0.860465
9 ALA ILE ALA VAL 0.508197 0.7
10 LYS ALA SER VAL GLY 0.506849 0.860465
11 GLY THR LEU SER ASN ARG ALA SER LYS LEU 0.5 0.860465
12 ACE THR VAL ALA SER SER NH2 0.464789 0.923077
13 ASP GLN ILE ILE 0.460317 0.675
14 ALA ALA ALA 0.45283 0.675676
15 ALA ALA LEU ALA ALA LEU LEU ALA ALA 0.446154 0.789474
16 ILE LEU SER ALA LEU VAL GLY ILE VAL 0.444444 0.880952
17 ALA ALA ALA ALA 0.444444 0.675676
18 ALA ALA ALA ALA ALA ALA 0.444444 0.675676
19 ALA ALA ALA ALA ALA ALA ALA 0.444444 0.675676
20 ALA LEU ALA LEU 0.421875 0.789474
21 GLY ALA THR VAL 0.421875 0.829268
22 ALA SER ASN SER ILE ALA SER GLY 0.421687 0.76087
23 ALA THR ALA ALA 0.419355 0.763158
24 SER LYS SER MLZ ASP ARG LYS TYR THR LEU 0.416667 0.734694
25 GLU GLU ILE ASP VAL VAL SER VAL 0.409091 0.840909
26 GLY CYS VAL LEU SER 0.405405 0.837209
27 ALA GLU ASP ASP VAL GLU 0.4 0.72093
28 ALA ALA GLY ILE GLY ILE LEU THR VAL 0.4 0.818182
29 GLU THR LEU GLU ASP SER VAL PHE 0.4 0.880952
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VNF; Ligand: VAL THR SER VAL VAL; Similar sites found: 79
This union binding pocket(no: 1) in the query (biounit: 5vnf.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3JU6 ANP 0.01157 0.4046 2.97297
2 4WOE ADP 0.0007029 0.46752 3.18471
3 3NTD COA 0.03329 0.40759 3.18471
4 4L4J NAG NAG BMA MAN NAG 0.00198 0.44339 4.4586
5 5KJW 53C 0.004178 0.43277 4.4586
6 5H2U 1N1 0.0005775 0.43113 4.86891
7 3NZ1 3NY 0.001475 0.45245 4.98084
8 2D6M LBT 0.001936 0.42751 5.03145
9 3A16 PXO 0.007338 0.41065 5.09554
10 2H8H H8H 0.001009 0.40872 5.09554
11 1W6O LAT 0.005682 0.40981 5.22388
12 5D9G GLU ASN LEU TYR PHE GLN 0.004521 0.41947 5.28455
13 4K55 H6P 0.0001763 0.50487 5.64516
14 5HES 032 0.0004415 0.48759 5.73248
15 4OMJ 2TX 0.006351 0.44425 5.73248
16 3WV6 GAL GLC 0.0006738 0.43751 5.73248
17 1M15 ADP 0.01519 0.42559 5.73248
18 1M15 ARG 0.01519 0.42559 5.73248
19 3WV6 GAL BGC 0.002669 0.42406 5.73248
20 2VFT SOR 0.005671 0.40646 5.73248
21 4Y24 TD2 0.002907 0.42176 5.84416
22 4DE9 VTP 0.01409 0.42376 5.94406
23 3OYW TDG 0.0009132 0.45855 5.97015
24 1GZW GAL BGC 0.004448 0.41689 5.97015
25 4XV1 904 0.002478 0.46556 6.16438
26 2QL9 CIT 0.004207 0.4289 6.18557
27 1JL0 PUT 0.002128 0.43866 6.28743
28 5LRT ADP 0.01133 0.42185 6.36943
29 3OPT AKG 0.01483 0.40365 6.70241
30 1A78 TDG 0.0005242 0.47302 6.71642
31 1SLT NDG GAL 0.001712 0.44049 6.71642
32 3SAO DBH 0.00005582 0.53274 6.875
33 4DSU BZI 0.0005783 0.47641 6.87831
34 3QPB URA 0.006816 0.41772 7.00637
35 4KBA 1QM 0.004115 0.42142 7.25076
36 1GQG DCD 0.008958 0.42388 7.42857
37 4RDL FUC GAL NDG FUC 0.01404 0.40208 7.64331
38 2YMZ LAT 0.0007684 0.43426 7.69231
39 5DYO FLU 0.01111 0.40948 7.79817
40 3QXV MTX 0.01768 0.40208 7.93651
41 3QRC SCR 0.005969 0.40083 8.9172
42 3ZJX BOG 0.004629 0.42752 8.99654
43 5T7I LAT NAG GAL 0.009874 0.41083 9.03226
44 3GC8 B45 0.00007959 0.4232 9.45946
45 4YLZ LAT NAG GAL 0.00823 0.41297 9.80392
46 3M3E GAL A2G NPO 0.0127 0.40733 9.93789
47 3WG3 A2G GAL NAG FUC 0.005423 0.41571 10.1124
48 5MJA 7O3 0.0005637 0.43091 10.1911
49 4Q0L V14 0.01265 0.4194 10.1911
50 3JQ3 ADP 0.005993 0.40523 10.1911
51 5H2D ERG 0.02136 0.4048 10.1911
52 1WW5 SGA BGC 0.005524 0.42256 11.25
53 1QKQ MAN 0.00006497 0.49493 11.2676
54 5FUI APY 0.004162 0.44696 11.3636
55 4TW7 37K 0.02332 0.40723 11.7188
56 1GT4 UNA 0.0008252 0.41861 11.9497
57 1LSH PLD 0.01919 0.41555 12.1019
58 1DZK PRZ 0.0006914 0.4217 12.7389
59 1N07 FMN 0.006919 0.44231 12.8834
60 2GQR ADP 0.01427 0.40472 13.0802
61 1I7M PUT 0.004193 0.41479 13.4328
62 1MDC PLM 0.002571 0.45116 13.6364
63 2OVD DAO 0.01483 0.40196 13.7363
64 5H9P TD2 0.004964 0.42262 13.9241
65 5H9Q TD2 0.0004599 0.45387 14.1935
66 3KFF XBT 0.0003389 0.47957 14.1975
67 3KFF ZBT 0.0003389 0.47957 14.1975
68 2G30 ALA ALA PHE 0.0007056 0.41665 14.3411
69 4XMF HSM 0.004259 0.40058 14.6739
70 1Y7P RIP 0.0001147 0.47806 15.9236
71 4WVW SLT 0.001456 0.43706 16.6667
72 5I0U DCY 0.01123 0.40316 17.1975
73 3CBC DBS 0.006631 0.42021 17.6768
74 3VV1 GAL FUC 0.002378 0.4364 18.75
75 5EOB 5QQ 0.01288 0.445 19.7492
76 4PSB GA3 0.0266 0.41276 20
77 3MTX PGT 0.02977 0.40795 24.5033
78 5KEW 6SB 0.002168 0.44323 31.9149
79 4LOO SB4 0.00006179 0.448 41.3793
Feedback