Receptor
PDB id Resolution Class Description Source Keywords
4B52 1.76 Å EC: 3.4.24.4 CRYSTAL STRUCTURE OF GENTLYASE, THE NEUTRAL METALLOPROTEASE PAENIBACILLUS POLYMYXA PAENIBACILLUS POLYMYXA HYDROLASE THERMOLYSIN LIKE PROTEASE
Ref.: STRUCTURE OF GENTLYASE, THE NEUTRAL METALLOPROTEASE PAENIBACILLUS POLYMYXA ACTA CRYSTALLOGR.,SECT.D V. 69 24 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:402;
B:403;
B:404;
A:402;
A:403;
A:404;
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
40.078 Ca [Ca+2...
RDF B:501;
A:501;
Valid;
Valid;
none;
none;
submit data
543.504 C23 H34 N3 O10 P C[C@H...
ZN B:401;
A:401;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
NA A:1305;
Part of Protein;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4B52 1.76 Å EC: 3.4.24.4 CRYSTAL STRUCTURE OF GENTLYASE, THE NEUTRAL METALLOPROTEASE PAENIBACILLUS POLYMYXA PAENIBACILLUS POLYMYXA HYDROLASE THERMOLYSIN LIKE PROTEASE
Ref.: STRUCTURE OF GENTLYASE, THE NEUTRAL METALLOPROTEASE PAENIBACILLUS POLYMYXA ACTA CRYSTALLOGR.,SECT.D V. 69 24 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4B52 - RDF C23 H34 N3 O10 P C[C@H]1[C@....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4B52 - RDF C23 H34 N3 O10 P C[C@H]1[C@....
50% Homology Family (97)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1LNC - VAL LYS n/a n/a
2 4MXJ - 2G8 C18 H30 N3 O5 P CCCNC(=O)[....
3 5JT9 Kd = 0.233 uM 7AF C21 H36 N3 O5 P C[C@H](CNC....
4 2TMN Ki = 1.3 uM 0FA C6 H15 N2 O4 P CC(C)C[C@@....
5 5LIF Kd = 1.34 uM 6XO C24 H38 N3 O7 P CC(C)C[C@@....
6 1GXW - VAL LYS n/a n/a
7 1PE8 - BR5 LEU LEN n/a n/a
8 6D5T - VAL LYS n/a n/a
9 5N31 - 8LB C21 H35 N4 O7 P CC(C)C[C@@....
10 5N2X - 8KN C20 H33 N4 O7 P CC(C)C[C@@....
11 1LNE - VAL LYS n/a n/a
12 1Y3G Ki = 40 nM 3PL AMM LEU n/a n/a
13 1HYT - BZS C11 H12 O4 c1ccc(cc1)....
14 1LNB - VAL LYS n/a n/a
15 3MSA - B3R C6 H5 Br O c1cc(cc(c1....
16 5L41 Kd = 0.31 uM 6QC C21 H36 N3 O5 P C[C@@H](CN....
17 5WR2 - NX6 C12 H13 N O6 c1ccc(cc1)....
18 1KKK - PHQ ASP n/a n/a
19 5WR5 - NX6 C12 H13 N O6 c1ccc(cc1)....
20 1KR6 - PHQ DGL n/a n/a
21 2TLX - VAL LYS n/a n/a
22 1PE5 - BR3 LEU LEN n/a n/a
23 4N4E - 2G6 C21 H36 N3 O5 P CC(C)C[C@@....
24 5N34 - 8JQ C17 H29 N4 O5 P CC(C)C[C@@....
25 1LNA - VAL LYS n/a n/a
26 3ZI6 - VAL LYS n/a n/a
27 4TMN Ki = 0.068 nM 0PK C25 H34 N3 O7 P NULL
28 6D5R - VAL LYS n/a n/a
29 5TMN Ki = 9.1 nM 0PJ C21 H34 N3 O7 P NULL
30 3NN7 - BXA C2 H3 Br O2 C(C(=O)O)B....
31 1ZDP Ki = 1.8 uM TIO C12 H15 N O3 S c1ccc(cc1)....
32 1FJT - VAL LYS n/a n/a
33 3MSN - NMU C2 H6 N2 O CNC(=O)N
34 4TLN Ki = 190 uM LNO C6 H14 N2 O2 CC(C)C[C@@....
35 4MWP - 2GC C23 H32 N3 O5 P CC(C)C[C@@....
36 1QF0 Ki = 42 nM TI2 C27 H28 N2 O5 S c1ccc(cc1)....
37 6D5S - VAL LYS n/a n/a
38 1KRO - PHQ DTH n/a n/a
39 1KJP - PHQ GLU n/a n/a
40 1KL6 - PHQ ALA n/a n/a
41 1Z9G Ki = 2.3 uM RRT C12 H15 N O3 S c1ccc(cc1)....
42 4MZN - 2G9 C20 H34 N3 O5 P CC[C@H](C)....
43 5WR6 - NX6 C12 H13 N O6 c1ccc(cc1)....
44 6FSM - VAL LYS n/a n/a
45 1QF2 Ki = 1200 nM TI3 C22 H24 N2 O4 S c1ccc(cc1)....
46 1KJO - PHQ THR n/a n/a
47 1KTO - PHQ DAL n/a n/a
48 1PE7 - 4BR LEU LEN n/a n/a
49 3TMN - VAL TRP n/a n/a
50 5N2Z - 8JH C19 H33 N4 O5 P CC(C)C[C@@....
51 5JVI Kd = 0.31 uM 6QC C21 H36 N3 O5 P C[C@@H](CN....
52 8TLN - VAL LYS n/a n/a
53 5M9W Kd = 5.7 mM 7GR C17 H26 N3 O7 P CC(C)C[C@@....
54 1LNF - VAL LYS n/a n/a
55 3F28 - S7B C12 H12 O4 Cc1cccc(c1....
56 5WR3 - NX6 C12 H13 N O6 c1ccc(cc1)....
57 4OI5 - 2G6 C21 H36 N3 O5 P CC(C)C[C@@....
58 1QF1 Ki = 48 nM TI1 C19 H28 N2 O4 S CCCCC[C@@H....
59 1TLP Ki = 28 nM RDF C23 H34 N3 O10 P C[C@H]1[C@....
60 5N2T - 8KK C18 H31 N4 O5 P CC(C)C[C@@....
61 3FCQ Ki = 1.7 mM M3S C10 H10 O4 Cc1cccc(c1....
62 5JS3 Kd = 0.185 uM 6MG C22 H38 N3 O5 P C[C@H](CNC....
63 5M5F Kd = 5.7 mM 7GR C17 H26 N3 O7 P CC(C)C[C@@....
64 5LVD Kd = 2.4 mM 79F C18 H28 N3 O8 P CC(C)C[C@@....
65 5MA7 Kd = 0.336 mM 7K0 C18 H29 N4 O7 P CC(C)C[C@@....
66 1TLX - VAL LYS n/a n/a
67 6D5Q - VAL LYS n/a n/a
68 5N3V - 8L5 C16 H30 N4 O5 P [H].[H].[H....
69 5TLN Ki = 0.43 uM BAN C21 H23 N5 O7 C[C@@H](C(....
70 5L8P Kd = 0.185 uM 6MG C22 H38 N3 O5 P C[C@H](CNC....
71 5L3U Kd = 0.354 uM 6NG C22 H38 N3 O5 P C[C@@H](CN....
72 6D5N - VAL LYS n/a n/a
73 5MNR - JC2 C19 H31 N4 O7 P CC(C)C[C@@....
74 6D5U - VAL LYS n/a n/a
75 1TMN Ki = 50 nM 0ZN C27 H33 N3 O5 CC(C)C[C@@....
76 3F2P - S3B C11 H12 O4 CCC(=O)Oc1....
77 1THL Ki = 0.38 uM 0DB C28 H32 N2 O5 NULL
78 1OS0 Ki = 0.93 uM 0PQ C27 H31 N2 O5 P c1ccc(cc1)....
79 5JXN Kd = 0.388 uM 6NN C20 H34 N3 O5 P CC[C@@H](C....
80 6FJ2 - VAL LYS n/a n/a
81 6TMN - 0PI C21 H33 N2 O8 P NULL
82 6D5O - VAL LYS n/a n/a
83 1KS7 - PHQ DAS n/a n/a
84 5DPE - 5H8 C21 H34 N3 O7 P CC(C)C[C@@....
85 5LWD Kd = 0.57 uM 79E C21 H35 N4 O6 P CC(C)C[C@@....
86 4N66 - 2GZ C20 H34 N3 O5 P CC(C)C[C@@....
87 1LND - VAL LYS n/a n/a
88 5DPF - 5H9 C22 H36 N3 O7 P CC(C)C[C@@....
89 5FXN - VAL LYS n/a n/a
90 5N3Y - 8L2 C18 H29 N4 O7 P CC(C)C[C@@....
91 5M69 Kd = 5.7 mM 7GR C17 H26 N3 O7 P CC(C)C[C@@....
92 1KEI - VAL LYS n/a n/a
93 4N5P - 2H0 C20 H34 N3 O5 P CC(C)CCNC(....
94 4MTW - 2G7 C19 H32 N3 O5 P CC(C)C[C@@....
95 5JSS Kd = 0.354 uM 6NG C22 H38 N3 O5 P C[C@@H](CN....
96 5A3Y - VAL LYS n/a n/a
97 4B52 - RDF C23 H34 N3 O10 P C[C@H]1[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RDF; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 RDF 1 1
2 0ZN 0.509259 0.632353
3 FLX 0.405172 0.820895
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4B52; Ligand: RDF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4b52.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4B52; Ligand: RDF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4b52.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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