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 (88)
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 5N31 - 8LB C21 H35 N4 O7 P CC(C)C[C@@....
9 5N2X - 8KN C20 H33 N4 O7 P CC(C)C[C@@....
10 1LNE - VAL LYS n/a n/a
11 1Y3G Ki = 40 nM 3PL AMM LEU n/a n/a
12 1HYT - BZS C11 H12 O4 c1ccc(cc1)....
13 1LNB - VAL LYS n/a n/a
14 3MSA - B3R C6 H5 Br O c1cc(cc(c1....
15 5L41 Kd = 0.31 uM 6QC C21 H36 N3 O5 P C[C@@H](CN....
16 5WR2 - NX6 C12 H13 N O6 c1ccc(cc1)....
17 1KKK - PHQ ASP n/a n/a
18 5WR5 - NX6 C12 H13 N O6 c1ccc(cc1)....
19 1KR6 - PHQ DGL n/a n/a
20 2TLX - VAL LYS n/a n/a
21 1PE5 - BR3 LEU LEN n/a n/a
22 4N4E - 2G6 C21 H36 N3 O5 P CC(C)C[C@@....
23 5N34 - 8JQ C17 H29 N4 O5 P CC(C)C[C@@....
24 1LNA - VAL LYS n/a n/a
25 3ZI6 - VAL LYS n/a n/a
26 4TMN Ki = 0.068 nM 0PK C25 H34 N3 O7 P NULL
27 5TMN Ki = 9.1 nM 0PJ C21 H34 N3 O7 P NULL
28 3NN7 - BXA C2 H3 Br O2 C(C(=O)O)B....
29 1ZDP Ki = 1.8 uM TIO C12 H15 N O3 S c1ccc(cc1)....
30 1FJT - VAL LYS n/a n/a
31 3MSN - NMU C2 H6 N2 O CNC(=O)N
32 4TLN Ki = 190 uM LNO C6 H14 N2 O2 CC(C)C[C@@....
33 4MWP - 2GC C23 H32 N3 O5 P CC(C)C[C@@....
34 1QF0 Ki = 42 nM TI2 C27 H28 N2 O5 S c1ccc(cc1)....
35 1KRO - PHQ DTH n/a n/a
36 1KJP - PHQ GLU n/a n/a
37 1KL6 - PHQ ALA n/a n/a
38 1Z9G Ki = 2.3 uM RRT C12 H15 N O3 S c1ccc(cc1)....
39 4MZN - 2G9 C20 H34 N3 O5 P CC[C@H](C)....
40 5WR6 - NX6 C12 H13 N O6 c1ccc(cc1)....
41 1QF2 Ki = 1200 nM TI3 C22 H24 N2 O4 S c1ccc(cc1)....
42 1KJO - PHQ THR n/a n/a
43 1KTO - PHQ DAL n/a n/a
44 1PE7 - 4BR LEU LEN n/a n/a
45 3TMN - VAL TRP n/a n/a
46 5N2Z - 8JH C19 H33 N4 O5 P CC(C)C[C@@....
47 5JVI Kd = 0.31 uM 6QC C21 H36 N3 O5 P C[C@@H](CN....
48 8TLN - VAL LYS n/a n/a
49 5M9W Kd = 5.7 mM 7GR C17 H26 N3 O7 P CC(C)C[C@@....
50 1LNF - VAL LYS n/a n/a
51 3F28 - S7B C12 H12 O4 Cc1cccc(c1....
52 5WR3 - NX6 C12 H13 N O6 c1ccc(cc1)....
53 4OI5 - 2G6 C21 H36 N3 O5 P CC(C)C[C@@....
54 1QF1 Ki = 48 nM TI1 C19 H28 N2 O4 S CCCCC[C@@H....
55 1TLP Ki = 28 nM RDF C23 H34 N3 O10 P C[C@H]1[C@....
56 5N2T - 8KK C18 H31 N4 O5 P CC(C)C[C@@....
57 3FCQ Ki = 1.7 mM M3S C10 H10 O4 Cc1cccc(c1....
58 5JS3 Kd = 0.185 uM 6MG C22 H38 N3 O5 P C[C@H](CNC....
59 5M5F Kd = 5.7 mM 7GR C17 H26 N3 O7 P CC(C)C[C@@....
60 5LVD Kd = 2.4 mM 79F C18 H28 N3 O8 P CC(C)C[C@@....
61 5MA7 Kd = 0.336 mM 7K0 C18 H29 N4 O7 P CC(C)C[C@@....
62 1TLX - VAL LYS n/a n/a
63 5N3V - 8L5 C16 H30 N4 O5 P [H].[H].[H....
64 5TLN Ki = 0.43 uM BAN C21 H23 N5 O7 C[C@@H](C(....
65 5L8P Kd = 0.185 uM 6MG C22 H38 N3 O5 P C[C@H](CNC....
66 5L3U Kd = 0.354 uM 6NG C22 H38 N3 O5 P C[C@@H](CN....
67 5MNR - JC2 C19 H31 N4 O7 P CC(C)C[C@@....
68 1TMN Ki = 50 nM 0ZN C27 H33 N3 O5 CC(C)C[C@@....
69 3F2P - S3B C11 H12 O4 CCC(=O)Oc1....
70 1THL Ki = 0.38 uM 0DB C28 H32 N2 O5 NULL
71 1OS0 Ki = 0.93 uM 0PQ C27 H31 N2 O5 P c1ccc(cc1)....
72 5JXN Kd = 0.388 uM 6NN C20 H34 N3 O5 P CC[C@@H](C....
73 6TMN - 0PI C21 H33 N2 O8 P NULL
74 1KS7 - PHQ DAS n/a n/a
75 5DPE - 5H8 C21 H34 N3 O7 P CC(C)C[C@@....
76 5LWD Kd = 0.57 uM 79E C21 H35 N4 O6 P CC(C)C[C@@....
77 4N66 - 2GZ C20 H34 N3 O5 P CC(C)C[C@@....
78 1LND - VAL LYS n/a n/a
79 5DPF - 5H9 C22 H36 N3 O7 P CC(C)C[C@@....
80 5FXN - VAL LYS n/a n/a
81 5N3Y - 8L2 C18 H29 N4 O7 P CC(C)C[C@@....
82 5M69 Kd = 5.7 mM 7GR C17 H26 N3 O7 P CC(C)C[C@@....
83 1KEI - VAL LYS n/a n/a
84 4N5P - 2H0 C20 H34 N3 O5 P CC(C)CCNC(....
85 4MTW - 2G7 C19 H32 N3 O5 P CC(C)C[C@@....
86 5JSS Kd = 0.354 uM 6NG C22 H38 N3 O5 P C[C@@H](CN....
87 5A3Y - VAL LYS n/a n/a
88 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: 55
This union binding pocket(no: 1) in the query (biounit: 4b52.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4DD8 BAT 0.001124 0.41485 1.92308
2 1BKC INN 0.0004635 0.46334 1.95312
3 1S17 GNR 0.002235 0.40438 2.22222
4 2XQ0 BES 0.00127 0.41946 2.30263
5 4DR9 BB2 0.002403 0.41779 2.60417
6 3DWB RDF 0.0000004129 0.58483 2.63158
7 2V57 PRL 0.0004295 0.48991 2.63158
8 2J83 BAT 0.002072 0.4013 2.67176
9 1R55 097 0.002621 0.4385 2.96053
10 1QJI PKF 0.001941 0.42155 3
11 3Q2H QHF 0.001885 0.40956 3.0303
12 3BQF SSM 0.008284 0.4247 3.09278
13 2GBB CIT 0.01251 0.40545 3.20513
14 1YP1 LYS ASN LEU 0.001077 0.46322 3.46535
15 4AIG FLX 0.009194 0.40756 3.48259
16 4GAA BES 0.001244 0.431 3.61842
17 1MMQ RRS 0.0001668 0.45911 4.11765
18 3AHO 3A2 0.0005825 0.47056 4.27632
19 1KAP GLY SER ASN SER 0.001013 0.43519 4.27632
20 1ATL 0QI 0.0006067 0.46603 4.45545
21 2W14 WR2 0.0007263 0.44921 4.45545
22 4QHP 32Q 0.001074 0.40613 4.60526
23 4MRP GSH 0.03305 0.40197 4.60526
24 4WKI 3PW 0.005915 0.41228 5.10638
25 5KD8 TNR 0.007663 0.42065 5.26316
26 1RM8 BAT 0.0006856 0.473 5.32544
27 1FBL HTA 0.001084 0.42985 5.92105
28 4DV8 0LX 0.001625 0.46255 6.25
29 3SVJ 4LI 0.01176 0.40418 6.40394
30 1G27 BB1 0.001733 0.40858 6.54762
31 3HBV ALA LYS ALA SER GLN ALA ALA 0.0003135 0.47117 6.57895
32 4IN9 SER TRP PHE PRO 0.001502 0.45911 7.22892
33 2ZXG S23 0.0002766 0.40266 7.23684
34 5U83 ZN8 0.01507 0.40592 7.54717
35 4K90 MLA 0.00002977 0.52479 7.56579
36 5KDX GAL TNR 0.01927 0.40309 7.56579
37 3M6P BB2 0.004659 0.41718 7.77202
38 1RL4 BRR 0.003978 0.43489 8.51064
39 1WS1 BB2 0.002722 0.41534 8.97436
40 2TCL RO4 0.0001423 0.44473 9.46746
41 3HY9 098 0.006333 0.41305 9.50226
42 4ARF IP8 GLY PRO ALA 0.0008962 0.43646 9.53947
43 5L44 K26 0.0008667 0.43639 9.86842
44 4WZV E40 0.0003699 0.40174 10
45 4AR8 IP8 GLY PRO ALA 0.0001491 0.47038 10.1974
46 3ZVS MLI 0.001087 0.44353 10.625
47 1LQY BB2 0.002508 0.40898 10.8696
48 4RHS SIA SIA GAL 0.01961 0.41577 11.4754
49 1Y79 LYS TRP 0.0001959 0.44986 13.1579
50 3D3X ARG ILE MET GLU NH2 0.0007384 0.40829 14.1447
51 3E3U NVC 0.002016 0.42924 15.2284
52 4KX8 L2O VAL VAL ASP 0.0001548 0.44423 15.4605
53 1L0I PSR 0.02045 0.40203 16.6667
54 1Q3A NGH 0.001051 0.45777 16.9697
55 3DBK RDF 0.0000000000003337 0.78986 41.5282
Pocket No.: 2; Query (leader) PDB : 4B52; Ligand: RDF; Similar sites found: 10
This union binding pocket(no: 2) in the query (biounit: 4b52.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5W3Y ACO 0.02578 0.40202 3.28947
2 5KOD IAC 0.003765 0.40144 3.61842
3 2X1E X1E 0.01533 0.40628 3.94737
4 5BRP PNG 0.01571 0.40058 4.60526
5 4UP4 NAG 0.01726 0.41276 4.93421
6 4UP4 NDG 0.01726 0.41276 4.93421
7 1Q1Y BB2 0.009857 0.40026 5.2356
8 2HI4 BHF 0.004015 0.40898 5.26316
9 1O68 KIV 0.003437 0.44033 5.45455
10 2GVY BGC GLC 0.01919 0.41751 6.90789
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