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Receptor
PDB id Resolution Class Description Source Keywords
5JWI 2.1 Å EC: 3.4.14.- CRYSTAL STRUCTURE OF PORPHYROMONAS ENDODONTALIS DPP11 IN COM DIPEPTIDE ARG-GLU PORPHYROMONAS ENDODONTALIS PEPTIDASE BACTERIAL ENZYME DIPEPTIDE HYDROLASE
Ref.: BACTERIAL PROTEASE USES DISTINCT THERMODYNAMIC SIGN FOR SUBSTRATE RECOGNITION. SCI REP V. 7 2848 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG GLU A:801;
B:803;
Valid;
Valid;
none;
none;
submit data
303.319 n/a O=C([...
CL B:801;
B:802;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JWI 2.1 Å EC: 3.4.14.- CRYSTAL STRUCTURE OF PORPHYROMONAS ENDODONTALIS DPP11 IN COM DIPEPTIDE ARG-GLU PORPHYROMONAS ENDODONTALIS PEPTIDASE BACTERIAL ENZYME DIPEPTIDE HYDROLASE
Ref.: BACTERIAL PROTEASE USES DISTINCT THERMODYNAMIC SIGN FOR SUBSTRATE RECOGNITION. SCI REP V. 7 2848 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5JWG - ARG ASP n/a n/a
2 5JWI - ARG GLU n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5JWG - ARG ASP n/a n/a
2 5JWI - ARG GLU n/a n/a
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5JWG - ARG ASP n/a n/a
2 5JWI - ARG GLU n/a n/a
3 5JXF - ARG ASP n/a n/a
4 3WON Ki = 0.41 mM VAL TYR n/a n/a
5 3WOP - VAL TYR ILE HIS PRO PHE n/a n/a
6 3WOL Ki = 0.41 mM VAL TYR n/a n/a
7 3WOQ - VAL TYR ILE HIS PRO PHE n/a n/a
8 3WOM Ki = 0.41 mM VAL TYR n/a n/a
9 4Y06 - LEU GLU n/a n/a
10 3WOO - VAL TYR ILE HIS PRO PHE n/a n/a
11 3WOR - ASP ARG VAL TYR ILE HIS PRO PHE n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG GLU; Similar ligands found: 39
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG GLU 1 1
2 ARG GLU ALA ALA 0.636364 0.953488
3 ARG SER ARG 0.622951 0.851064
4 ARG VAL 0.568965 0.886364
5 ALA ARG 0.561404 0.928571
6 ARG ASP 0.55 0.97619
7 LYS ARG LYS 0.537313 0.930233
8 ARG ASP ALA ALA 0.537313 0.953488
9 ASP GLU 0.537037 0.714286
10 ARG ARG ALA ALA 0.529412 0.909091
11 ALA DGL 0.509434 0.714286
12 LEU GLU 0.508772 0.666667
13 ARG LEU GLY GLU SER 0.492537 0.826087
14 ARG ILE MET GLU NH2 0.487805 0.836735
15 ARG ARG ARG ARG ARG ARG ARG ARG 0.478261 0.883721
16 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.478261 0.883721
17 ARG GLY ASP 0.478261 0.953488
18 ARG GLY THR 0.478261 0.891304
19 MET ALA ARG 0.472222 0.833333
20 ARG ARG GLY CYS NH2 0.464789 0.866667
21 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.456522 0.788462
22 LYS GLU LYS 0.454545 0.813953
23 ARG ARG GLY LEU NH2 0.452055 0.829787
24 ARG ARG GLY ILE NH2 0.445946 0.829787
25 ARG ASP ARG ALA ALA LYS LEU 0.444444 0.851064
26 GLU ALY ARG 0.444444 0.891304
27 THR ALA ARG M3L SER THR 0.441558 0.65
28 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.441176 0.62963
29 ARG ALA ARG 0.434783 0.860465
30 BEZ NLE LYS ARG OAR 0.434783 0.857143
31 ARG ARG GLY MET NH2 0.428571 0.78
32 ARG ILE ALA ALA ALA 0.428571 0.822222
33 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.428571 0.863636
34 LYS LYS 0.423729 0.767442
35 GLU ARG GLY SER GLY ARG 0.418605 0.836735
36 ARG ARG ARG GLU THR GLN VAL 0.418605 0.803922
37 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.416667 0.930233
38 GLU ARG GLY MET THR 0.41573 0.788462
39 GLN LYS 0.40625 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JWI; Ligand: ARG GLU; Similar sites found with APoc: 76
This union binding pocket(no: 1) in the query (biounit: 5jwi.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 2ZJ1 NAD 2.22222
2 2ZJ1 ARJ 2.22222
3 2VAR KDG 2.23642
4 2VAR KDF 2.23642
5 1Q8A HCS 2.4735
6 5KWW 6YA 2.99296
7 5TXR PLP 3.05499
8 2OUA AES 3.19149
9 4YLU R30 3.26797
10 2ANY BAM 3.3195
11 4YOI 4F4 3.59477
12 2AIQ BEN 3.8961
13 1SQA UI1 4.08163
14 5A8Y VBM 4.12844
15 1FIW PBZ 4.13793
16 4O48 ASP 4.21687
17 1GJC 130 4.34783
18 5H6S HDH 4.3659
19 2CDO GAL AAL GAL AAL GAL AAL 4.375
20 3N7O N7O 4.42478
21 4M3P HCS 4.4335
22 6B74 BEN 4.52675
23 1HPG BOC ALA ALA PRO GLU 4.81283
24 5WB6 9ZM 4.91803
25 5Q0F 9FA 4.91803
26 4O97 NTX 4.97925
27 6BQK Z1E 5.02283
28 1U1I NAD 5.10204
29 1T32 OHH 5.35714
30 5GVR LMR 5.55556
31 2XCF BBQ 5.55556
32 1RTF BEN 5.95238
33 2H9E DTY ILE ARG LEU LPD 6.00858
34 4ISS TAR 6.21118
35 5ZFI 9C9 6.25
36 1YF4 CYS TYR PHE GLN ASN CYS PRO ARG GLY NH2 6.27803
37 1A0J BEN 6.27803
38 1IAU ACE ILE GLU PRO ASJ 6.60793
39 1SL3 170 6.62021
40 2O66 FLC 6.66667
41 5FAH 5VT 6.69643
42 2OEM 1AE 6.77966
43 1XUJ BOZ 7.17489
44 5NB7 8NQ 7.3913
45 1PQ7 ARG 7.58929
46 5EGM 5NY 7.65957
47 2XYA 7L4 7.69231
48 4YJK URA 7.93651
49 3MMG GLU THR VAL ARG PHE GLN SER ASP 8.29876
50 2NLQ GLY 8.33333
51 1N62 MCN 8.43373
52 4SGA ACE PRO ALA PRO PHE 8.83978
53 4NFE BEN 8.86076
54 2B7D C1B 9.17431
55 2MBR EPU 9.41177
56 2MBR FAD 9.41177
57 2BDG PBZ 9.41704
58 2P8O BVA 10.3093
59 1T3Q MCN 10.7143
60 3KEE 30B 11.0526
61 1YGC 905 11.1111
62 3P8N L4T 11.828
63 5L2Z 70C 12.069
64 1V1A KDG 12.2977
65 3SUD SUE 14.2857
66 4BTI 7R9 14.5833
67 2PKA BEN 16.25
68 2EC9 24X 17.3333
69 4D8N 0HM 17.9372
70 1TMT DPN PRO ARG 19.4444
71 2ANM CDO 19.4444
72 1A2C 34H LEU PRJ OAR 19.4444
73 3VXE DPN PRO ARG 19.4444
74 3BPX SAL 22.2973
75 4AX9 N5N 25
76 1EB1 ZAL PRO MMO 25.9259
Pocket No.: 2; Query (leader) PDB : 5JWI; Ligand: ARG GLU; Similar sites found with APoc: 8
This union binding pocket(no: 2) in the query (biounit: 5jwi.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 3W8X FAD 2.35043
2 2WOX NDP 3.88548
3 4CU1 H4B 4.06321
4 5ZXD ATP 4.21245
5 3B9Q MLI 5.29801
6 3BOF HCS 6.71378
7 3AB4 THR 6.74157
8 4A3X LAT 8.37004
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