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Receptor
PDB id Resolution Class Description Source Keywords
6CD8 1.6 Å NON-ENZYME: OTHER COMPLEX OF GID4 FRAGMENT WITH SHORT PEPTIDE HOMO SAPIENS STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC PEBINDING PROTEIN
Ref.: MOLECULAR BASIS OF GID4-MEDIATED RECOGNITION OF DEG THE PRO/N-END RULE PATHWAY. NAT. CHEM. BIOL. V. 14 466 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UNX A:301;
A:308;
A:307;
B:304;
A:303;
B:305;
A:310;
B:303;
A:305;
A:302;
B:301;
B:306;
B:307;
B:308;
B:302;
A:306;
A:309;
A:311;
A:304;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
n/a X *
PRO SER ARG VAL C:1;
D:1;
Valid;
Valid;
none;
Atoms found LESS than expected: % Diff = 0.125;
Kd = 19.4 uM
458.54 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6CDG 1.6 Å NON-ENZYME: OTHER GID4 FRAGMENT IN COMPLEX WITH A PEPTIDE HOMO SAPIENS STRUCTURAL GENOMICS CONSORTIUM SGC PEPTIDE BINDING PROTEIN
Ref.: MOLECULAR BASIS OF GID4-MEDIATED RECOGNITION OF DEG THE PRO/N-END RULE PATHWAY. NAT. CHEM. BIOL. V. 14 466 2018
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 6CD8 Kd = 19.4 uM PRO SER ARG VAL n/a n/a
2 6CDG Kd = 1.9 uM PRO GLY LEU TRP LYS SER n/a n/a
3 6CD9 - PRO SER ARG TRP n/a n/a
4 6CDC Kd = 2.5 uM PRO GLY LEU TRP n/a n/a
5 6CCT - PRO THR LEU VAL n/a n/a
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 6CCU Kd = 35.2 uM PRO HIS ARG VAL n/a n/a
2 6CD8 Kd = 19.4 uM PRO SER ARG VAL n/a n/a
3 6CDG Kd = 1.9 uM PRO GLY LEU TRP LYS SER n/a n/a
4 6CD9 - PRO SER ARG TRP n/a n/a
5 6CDC Kd = 2.5 uM PRO GLY LEU TRP n/a n/a
6 6CCT - PRO THR LEU VAL n/a n/a
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 6CCU Kd = 35.2 uM PRO HIS ARG VAL n/a n/a
2 6CD8 Kd = 19.4 uM PRO SER ARG VAL n/a n/a
3 6CDG Kd = 1.9 uM PRO GLY LEU TRP LYS SER n/a n/a
4 6CD9 - PRO SER ARG TRP n/a n/a
5 6CDC Kd = 2.5 uM PRO GLY LEU TRP n/a n/a
6 6CCT - PRO THR LEU VAL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PRO SER ARG VAL; Similar ligands found: 43
No: Ligand ECFP6 Tc MDL keys Tc
1 PRO SER ARG VAL 1 1
2 PRO SER ARG TRP 0.588235 0.83871
3 THR PRO THR ARG ASP VAL ALA THR SER PRO 0.487395 0.833333
4 PRO SER ILE ASP ARG SER THR LYS PRO 0.484375 0.794118
5 PRO HIS ARG VAL 0.474747 0.725806
6 PRO LEU SER LYS 0.473118 0.859649
7 PRO VAL LYS ARG ARG LEU ASP LEU GLU 0.470588 0.864407
8 ARG ARG ARG GLU THR GLN VAL 0.464646 0.79661
9 VAL ALA ARG SER 0.460674 0.836364
10 PRO SER M3L PHE NLW 0.457944 0.695652
11 LEU PRO PRO GLU GLU ARG LEU ILE 0.457627 0.757576
12 SER PRO ARG LEU PRO LEU LEU GLU SER 0.455357 0.75
13 PRO PRO LYS ARG ILE ALA 0.453782 0.753846
14 LYS GLY PRO PRO LEU PRO ARG PRO ARG VAL 0.45045 0.738462
15 PRO THR SER SER GLU GLN ILE 0.447619 0.8
16 PRO ILE VAL 0.445783 0.77193
17 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.445545 0.813559
18 PRO GLN ILE ILE ASN ARG PRO GLN ASN 0.445378 0.731343
19 PRO LEU GLU PSA ARG LEU 0.44 0.885246
20 PRO ARG ARG PRO VAL ILE MET ARG ARG 0.44 0.685714
21 VAL ARG SER ARG ARG ABA LEU ARG LEU 0.436893 0.813559
22 CYS THR PRO SER ARG 0.436364 0.828125
23 LYS ARG ARG LYS SEP VAL 0.435644 0.734375
24 ALA ARG 9AT 0.428571 0.803571
25 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.427273 0.783333
26 ARG VAL 0.425 0.763636
27 ALA ASN SER ARG VAL PRO THR SER ILE ILE 0.422764 0.846154
28 ALA PRO ALA LEU ARG VAL VAL LYS 0.421569 0.77193
29 ARG SER ARG 0.418605 0.803571
30 ARG GLU ARG SER PRO THR ARG 0.415094 0.825397
31 MBN ABN RNG GLY VAL ARG 0.411765 0.769231
32 PRO THR VAL GLU GLU VAL ASP 0.411765 0.827586
33 GLY LEU LEU GLY SER PRO VAL ARG ALA 0.41129 0.857143
34 SER PRO HIS ASN PRO ILE SER SEP VAL SEP 0.411215 0.769231
35 SER HIS PRO ARG PRO ILE ARG VAL 0.409091 0.797101
36 ILE GLN GLN SER ILE GLU ARG ILE 0.409091 0.79661
37 SER PRO LYS ARG ILE ALA 0.408696 0.84127
38 PRO PRO PRO VAL PRO PRO ARG ARG ARG ARG 0.408696 0.75
39 PRO ALA ILE ILE ASN ARG PRO GLN ASN 0.408333 0.731343
40 ALA ASN SER ARG VAL GLN ASP SER ILE ILE 0.40678 0.786885
41 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.403509 0.827586
42 ACE GLN GLU ARG GLU VAL PRO CYS 0.403361 0.769231
43 LYS PRO VAL LEU ARG THR ALA 0.4 0.84375
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6CDG; Ligand: PRO GLY LEU TRP LYS SER; Similar sites found with APoc: 129
This union binding pocket(no: 1) in the query (biounit: 6cdg.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 2HFN FMN None
2 4DDY DN6 1.1976
3 5NFB 8VT 1.1976
4 2B4B B33 1.79641
5 2Z77 NCA 2.15827
6 3WUC GLC GAL 2.18978
7 4BJ8 BTN 2.38095
8 4L4J NAG NAG BMA MAN NAG 2.39521
9 4COQ SAN 2.39521
10 5H4S RAM 2.39521
11 1T9M FMN 2.39521
12 1SLT NDG GAL 2.98507
13 1AUA BOG 2.99401
14 3HQP FDP 2.99401
15 2VQ5 HBA 2.99401
16 3ETH ATP 2.99401
17 4HAP CBI 2.99401
18 2A19 ANP 2.99401
19 6DND PLP 2.99401
20 4ITH RCM 2.99401
21 2HZY DHJ 2.99401
22 4MPO AMP 3.26797
23 5K21 6QF 3.5461
24 1MUU SUC 3.59281
25 4X5S AZM 3.59281
26 5GLT BGC GAL NAG GAL 3.59281
27 1SW0 PGA 3.59281
28 3X01 AMP 3.59281
29 4M2K PLP 3.59281
30 1DMY AZM 3.59281
31 3RGA LSB 3.59281
32 4FCW ADP 3.59281
33 3I4X DST 3.59281
34 5OUH L0B 3.59281
35 3GUZ PAF 3.59281
36 4AZ6 OAN 3.59281
37 4B74 1LH 3.59281
38 3WUD GLC GAL 3.67647
39 1IS3 LAT 3.7037
40 1GT4 UNA 3.77358
41 5AIG VPR 4
42 4Q0A 4OA 4.19162
43 3KV4 OGA 4.19162
44 2HXW FLC 4.19162
45 2AJH MET 4.19162
46 2AGC DAO 4.32099
47 3N9Q OGA 4.79042
48 3N9P OGA 4.79042
49 3N9O OGA 4.79042
50 1O5Q PYR 4.79042
51 6D3U 83Y BDP 83Y GCD 4.79042
52 6F90 MVL 4.79042
53 3FVQ ATP 4.79042
54 5ZMY TAR 4.79042
55 2D6M LBT 5.03145
56 1A78 TDG 5.22388
57 5GP0 GPP 5.36913
58 3CM2 X23 5.38462
59 4B7E OGA 5.38922
60 4XZ3 ACP 5.38922
61 1H2K OGA 5.38922
62 2XUM OGA 5.38922
63 4KYS VIB 5.38922
64 1H2M OGA 5.38922
65 3W9R A8S 5.38922
66 3P3N AKG 5.38922
67 3SI2 PBD 5.38922
68 3FW3 ETS 5.38922
69 2OO0 XAP 5.38922
70 4LHD GLY 5.38922
71 1TW4 CHD 5.6
72 1EC9 XYH 5.98802
73 3SBZ MLI 5.98802
74 1SO0 GAL 5.98802
75 1JG3 VAL TYR PRO IAS HIS ALA 5.98802
76 4B1L FRU 6.06061
77 5N0L ILE 6.28931
78 3IWD M2T 6.45161
79 2D2F ADP 6.58683
80 2AWN ADP 6.58683
81 2PCU ASP 6.58683
82 4NRT 2NG 6.58683
83 1QFT HSM 6.58683
84 4QDC ASD 7.18563
85 1SBR VIB 7.18563
86 3KDM TES 7.78443
87 3PB9 1BN 7.78443
88 5E62 Z3Q GAL 5N6 7.78443
89 5E65 5N6 GAL 7.78443
90 1DL7 NCH 8.03571
91 5AEW BNL 8.38323
92 4GN8 ASO 8.98204
93 2QUN FUD 8.98204
94 1SZ0 M6P 8.98204
95 5M6N 7H9 9.32203
96 5IN3 G1P 9.58084
97 4G7A AZM 9.58084
98 3WMX THR 9.58084
99 4FAI PBD 10.1796
100 2EB5 OXL 10.1796
101 4F5Z BEZ 10.7784
102 3WWC BUA 10.7784
103 5U9J GER 10.7784
104 1Y0L HAN 11.3772
105 2YKL NLD 11.3772
106 3G0I VPR 12.5749
107 4RW3 IPD 12.5749
108 1NVM OXL 12.5749
109 2OUA AES 13.1737
110 2UZ2 BTN 13.8462
111 1M3U KPL 14.3713
112 5B09 4MX 14.4231
113 4PXE GLV 14.9701
114 1DTD GLU 16.3934
115 4PZ6 GMP 17.9641
116 5XKR BZE 18.239
117 2Y0I AKG 19.0476
118 3WV6 GAL BGC 19.7605
119 2C1Q BTN 19.8413
120 1XIM XYL 20.3593
121 5X7Q GLC GLC GLC GLC GLC 20.9581
122 5X7Q GLC GLC GLC GLC 20.9581
123 2BO4 FLC 20.9581
124 3JZ0 CLY 22.7545
125 2P7Q GG6 23.3083
126 1WBI BTN 24.8062
127 2QJY UQ2 25.7485
128 5JWP AKG 26.3158
129 4M1U A2G MBG 32.8571
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