Receptor
PDB id Resolution Class Description Source Keywords
2XS3 2.4 Å EC: 3.-.-.- STRUCTURE OF KARILYSIN CATALYTIC MMP DOMAIN TANNERELLA FORSYTHIA HYDROLASE BACTERIAL MMP VIRULENCE FACTOR METALLOPROTEASEDEPENDENT PEPTIDASE
Ref.: THE STRUCTURE OF THE CATALYTIC DOMAIN OF TANNERELLA FORSYTHIA KARILYSIN REVEALS IT IS A BACTERIAL XENOL ANIMAL MATRIX METALLOPROTEINASES. MOL.MICROBIOL. V. 79 119 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA PHE THR SER C:201;
D:201;
 Valid;
Valid;
 none;
none;
 submit data
409.463 n/a O=C(N...
TRS B:1305;
 Invalid;
 none;
 submit data
122.143 C4 H12 N O3 C(C(C...
ZN A:998;
A:999;
B:998;
B:999;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4IN9 1.55 Å EC: 3.-.-.- STRUCTURE OF KARILYSIN MMP-LIKE CATALYTIC DOMAIN IN COMPLEX INHIBITORY TETRAPEPTIDE SWFP TANNERELLA FORSYTHIA MATRIXIN METALLOPEPTIDASE METALLOPROTEASE HYDROLYTIC ENZYHYDROLASE
Ref.: STRUCTURE OF THE CATALYTIC DOMAIN OF THE TANNERELLA FORSYTHIA MATRIX METALLOPEPTIDASE KARILYSIN IN COMP A TETRAPEPTIDIC INHIBITOR. ACTA CRYSTALLOGR.,SECT.F V. 69 472 2013
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 312 families.
1 2XS4 - ALA PHE THR n/a n/a
2 4IN9 Ki = 10.7 uM SER TRP PHE PRO n/a n/a
3 2XS3 - ALA PHE THR SER n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 261 families.
1 2XS4 - ALA PHE THR n/a n/a
2 4IN9 Ki = 10.7 uM SER TRP PHE PRO n/a n/a
3 2XS3 - ALA PHE THR SER n/a n/a
50% Homology Family (165)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2XS4 - ALA PHE THR n/a n/a
2 4IN9 Ki = 10.7 uM SER TRP PHE PRO n/a n/a
3 2XS3 - ALA PHE THR SER n/a n/a
4 1D8M - BBH C19 H21 N3 O6 S COc1ccc(cc....
5 1BIW ic50 = 104 nM S80 C20 H37 N3 O6 CC(C)C[C@H....
6 4DPE - NGH C13 H20 N2 O5 S CC(C)C[N@]....
7 2D1O Ki = 0.02 uM FA4 C24 H42 N6 O3 [H]/N=C(/N....
8 1HY7 ic50 = 4090 nM MBS C20 H21 N O6 S COCC#CC[C@....
9 1BQO ic50 = 18.4 nM N25 C21 H27 N3 O8 S2 CC1(C[N@](....
10 2USN Ki = 0.31 uM IN8 C19 H18 N4 O3 S2 c1ccc(cc1)....
11 1B3D - S27 C20 H27 N2 O3 P CC(C)C[C@H....
12 1CIZ Ki = 36 nM DPS C28 H29 N3 O4 S c1ccc(cc1)....
13 1D8F ic50 = 18 nM SPI C20 H23 N3 O7 S COc1ccc(cc....
14 1HFS Ki = 2 nM L04 C43 H48 F N3 O5 CC(C)C[C@@....
15 1D7X - SPC C13 H19 N3 O6 S COc1ccc(cc....
16 1G05 ic50 = 3.1 nM BBH C19 H21 N3 O6 S COc1ccc(cc....
17 1B8Y Ki = 14 nM IN7 C19 H22 N2 O4 S c1ccc(cc1)....
18 1CAQ Ki = 19 nM DPS C28 H29 N3 O4 S c1ccc(cc1)....
19 1G4K - HQQ C17 H14 N2 O4 CC1(C(=O)N....
20 4JA1 - NGH C13 H20 N2 O5 S CC(C)C[N@]....
21 1G49 ic50 = 16 nM 111 C16 H25 N3 O7 S2 CCCCOc1ccc....
22 1SLN Ki = 0.23 uM INH C25 H35 N6 O4 C[C@H](C(=....
23 1C3I - TR1 C24 H31 N3 O4 S CC(C)[C@@H....
24 1USN Ki = 0.018 uM IN9 C13 H10 F5 N5 O2 S2 CNC(=O)[C@....
25 4G9L - NGH C13 H20 N2 O5 S CC(C)C[N@]....
26 3AYU - ILE SER TYR GLY ASN ASP ALA LEU MET PRO n/a n/a
27 5I4O - V28 C28 H35 N5 O9 S CC(C)[C@H]....
28 4GQL Ki = 0.26 nM R47 C35 H35 Br Cl N4 O10 P c1cc(cc(c1....
29 1UTT ic50 = 24 uM CP8 C19 H20 N2 O4 S C[N@@]1c2c....
30 5I0L ic50 = 18 nM H27 C34 H42 N4 O12 S2 CC(C)[C@H]....
31 4EFS Ki = 2.5 nM E37 C22 H20 N2 O4 S c1ccc(cc1)....
32 4GR3 Ki = 15.5 nM R45 C29 H32 Br N4 O10 P c1ccc(cc1)....
33 5CZM - R47 C35 H35 Br Cl N4 O10 P c1cc(cc(c1....
34 6RLY Ki = 17.5 uM K8T C21 H20 N2 O3 c1ccc(cc1)....
35 1Y93 Kd = 8 mM HAE C2 H5 N O2 CC(=O)NO
36 6RD0 Ki = 17.7 uM K0Q C17 H17 N3 O3 c1ccc2c(c1....
37 3TSK - QEG C29 H32 N4 O6 S c1ccc(cc1)....
38 2W0D ic50 ~ 2 nM CGS C18 H23 N3 O5 S CC(C)[C@H]....
39 3F16 Kd = 5.91 nM HS3 C10 H12 N2 O6 S COc1ccc(cc....
40 5D3C - 56O C30 H32 Cl N5 O10 c1cc(cc(c1....
41 3NX7 Kd = 7.88 nM NHK C11 H16 N2 O6 S COc1ccc(cc....
42 3N2U - D3X C17 H26 N2 O11 S COc1ccc(cc....
43 2OXW - ILE ALA GLY n/a n/a
44 3EHY Ki = 1.4 uM TBL C10 H13 N O5 S C[C@H](C(=....
45 1UTZ ic50 = 0.014 uM PF3 C25 H20 N2 O3 S c1ccc(cc1)....
46 3LKA Kd = 1.5 mM M4S C7 H9 N O3 S COc1ccc(cc....
47 3F19 Kd = 65.1 nM HS6 C8 H7 F N2 O4 S c1cc(ccc1F....
48 5L7F Ki = 0.9 nM R47 6PJ n/a n/a
49 6ENM - LPW C21 H19 N O5 S COc1ccc(cc....
50 3EHX Ki = 25 nM BDL C18 H21 N O4 S CC(C)C[C@H....
51 6EOX - BKW C21 H18 O5 S COc1ccc(cc....
52 2HU6 Kd = 154 uM 37A C20 H21 N3 O5 c1ccc(cc1)....
53 3N2V - JT5 C16 H18 N2 O5 S c1ccc(cc1)....
54 3F18 Kd = 39.5 nM HS5 C10 H11 F N2 O5 S c1cc(ccc1F....
55 4GR8 Ki = 14.7 nM R4C C25 H28 Br N4 O6 P C[C@@H](C(....
56 3F15 Kd = 7.88 nM HS1 C12 H16 N2 O7 S COc1ccc(cc....
57 6ELA - B9Z C24 H22 O5 S COc1ccc(cc....
58 5N5J - HAE C2 H5 N O2 CC(=O)NO
59 2OXZ - ILE ALA GLY n/a n/a
60 3LIK Ki = 1.92 nM EEG C29 H31 N3 O7 S c1ccc(cc1)....
61 5I43 - 67M C37 H47 N5 O13 S CC(C)[C@H]....
62 3F17 Kd = 2.36 nM HS4 C14 H14 N2 O4 S c1ccc(cc1)....
63 6EKN - B9N C24 H22 O7 S COc1ccc(cc....
64 5D2B - 56O C30 H32 Cl N5 O10 c1cc(cc(c1....
65 2WO8 ic50 = 0.52 uM 077 C17 H18 O3 c1ccc(cc1)....
66 1OS2 - HAE C2 H5 N O2 CC(=O)NO
67 4GR0 Ki = 0.28 nM R4B C31 H31 Br Cl N4 O6 P C[C@@H](C(....
68 2WOA ic50 = 1.15 uM 576 C18 H18 O3 c1ccc-2c(c....
69 3LK8 Kd = 19.7 nM Z79 C9 H12 N2 O5 S COc1ccc(cc....
70 5L79 Ki = 0.9 nM R47 6PJ n/a n/a
71 3F1A Kd = 61.1 nM HS7 C8 H8 N2 O4 S c1ccc(cc1)....
72 5N5K - HAE C2 H5 N O2 CC(=O)NO
73 2WO9 ic50 = 0.062 uM 068 C19 H20 O4 CC(=O)c1cc....
74 3LJG Ki = 18.6 nM EEF C25 H29 N3 O7 c1ccc(cc1)....
75 5I3M - 67F C28 H38 N4 O9 S2 CC(C)[C@@H....
76 1RMZ - NGH C13 H20 N2 O5 S CC(C)C[N@]....
77 3LIL Ki = 8.3 nM EEA C28 H29 Cl N4 O8 c1cc(cc(c1....
78 4I03 - L88 C58 H66 N4 O11 S2 c1ccc(cc1)....
79 1ROS ic50 = 0.0017 uM DEO C28 H25 N O6 CCOc1ccc(c....
80 5CXA - 55L C30 H31 Cl N4 O10 c1cc(cc(c1....
81 5I2Z - V24 C34 H41 N5 O12 S CC(C)[C@H]....
82 1JK3 - BAT C23 H31 N3 O4 S2 CC(C)C[C@H....
83 3LIR Ki = 119 nM EEC C22 H26 N4 O8 c1ccc(cc1)....
84 3TS4 Ki = 1.9 nM EEG C29 H31 N3 O7 S c1ccc(cc1)....
85 3KEJ Ki = 75.9 nM 3EJ C22 H17 F N6 O3 c1cc(cc(c1....
86 4L19 Ki = 0.8 uM 1UA C15 H16 N2 O S Cc1ccc(cc1....
87 5BOT ic50 = 39 uM 4UM C12 H12 N2 O3 CCOC(=O)c1....
88 3KRY ic50 = 0.1 nM 3KR C22 H23 F3 N2 O7 S COCCN1CCC(....
89 1XUD ic50 = 8 nM PB4 C22 H20 F2 N4 O2 Cc1cc(ccc1....
90 3I7I ic50 = 620 nM 518 C29 H29 N3 O5 CNC(=O)[C@....
91 3WV1 ic50 = 0.0039 nM WHH C26 H22 F N3 O6 COc1cccc(c....
92 5BPA ic50 = 0.001 uM 4UF C24 H22 N4 O5 CCOC(=O)c1....
93 4JPA ic50 = 3.3 nM AZ6 C21 H23 N7 O5 S C[C@]1(C(=....
94 5B5O ic50 = 1900 nM WMM C12 H11 N5 S2 c1ccc(cc1)....
95 2OW9 ic50 = 30 nM SP6 C21 H16 N2 O4 S c1ccc(cc1)....
96 3ELM Ki = 0.19 nM 24F C23 H30 N2 O7 S2 CCOc1ccc(c....
97 1CXV - CBP C19 H20 Cl N O6 S c1cc(ccc1O....
98 4A7B - 3W5 C27 H30 N2 O5 S c1cc(ccc1C....
99 3WV2 ic50 = 12 nM WGG C17 H15 N3 O3 COc1cccc(c....
100 4JP4 - AZ4 C19 H23 F4 N7 O5 S c1c(cnc(n1....
101 2OZR ic50 = 0.67 nM GG1 C26 H20 N2 O4 CN1c2ccc(c....
102 5UWK Ki = 2.3 nM 8OM C25 H27 N3 O5 S2 CC(C)[C@@H....
103 1YOU ic50 = 0.87 nM PFD C20 H19 F N2 O6 CCOCCC1(C(....
104 830C Ki = 0.52 nM RS1 C19 H20 Cl N O6 S c1cc(ccc1O....
105 5BOY ic50 = 2.5 uM 4UE C15 H15 N3 O2 CCOC(=O)c1....
106 3I7G ic50 = 430 nM 732 C20 H23 Cl N2 O3 CNC(=O)[C@....
107 1XUC ic50 = 72 nM PB3 C22 H22 N4 O2 Cc1cccc(c1....
108 1ZTQ ic50 = 1.3 nM 033 C26 H24 N2 O6 S CC(C)[C@@H....
109 456C Ki = 0.17 nM CBP C19 H20 Cl N O6 S c1cc(ccc1O....
110 1XUR ic50 = 6600 nM PB5 C18 H16 N6 O2 c1cc(cnc1)....
111 2D1N Ki = 0.007 uM FA4 C24 H42 N6 O3 [H]/N=C(/N....
112 3KEC ic50 = 58 nM 3KE C24 H21 N5 O4 COc1ccc(cc....
113 5UWM ic50 = 356 nM 8OA C25 H28 N4 O4 S CC(C)[C@H]....
114 3TVC Ki = 18 nM E3P C26 H26 N2 O4 c1ccc(cc1)....
115 3ZXH - E41 C20 H28 N2 O4 S CC(C)CCN([....
116 3KEK Ki = 4.4 nM 3EK C24 H26 F N5 O3 Cc1cc(cc(n....
117 3WV3 ic50 = 24 nM WLL C15 H13 N3 O3 S COc1cccc(c....
118 2YIG ic50 = 79.4 nM 5EL C28 H27 N3 O3 c1cc(ccc1C....
119 5B5P ic50 = 0.2 nM WNN C20 H18 N6 O3 S c1ccc2c(c1....
120 3LJZ Ki = 7.3 nM LA3 C27 H26 N2 O6 c1ccc2c(c1....
121 6HV2 - ILE MET ILE SER PHE n/a n/a
122 1MNC - PLH C18 H27 N3 O4 CC(C)C[C@H....
123 3DPE ic50 = 57 nM AXB C24 H21 N5 O6 S2 c1cc2c(cc1....
124 1I76 - BSI C22 H19 N O4 S c1ccc(cc1)....
125 1ZP5 ic50 = 1200 uM 2NI C17 H17 N3 O3 CN(CCOc1cc....
126 1JAP - PRO LEU GLY HOA n/a n/a
127 2OY2 - ILE ALA GLY n/a n/a
128 1I73 - PRO LEU PAT n/a n/a
129 3DNG ic50 = 7.4 nM AXA C22 H21 N5 O5 S c1cc2c(cc1....
130 1JAO Ki = 1.2 uM 0D3 C15 H21 N3 O3 S NULL
131 1ZS0 Ki = 0.7 uM EIN C17 H22 N O6 P S CC(C)[C@@H....
132 1BZS ic50 = 10 nM BSI C22 H19 N O4 S c1ccc(cc1)....
133 1JAQ Ki = 33 uM 01S C12 H22 N4 O5 NULL
134 1KBC - HLE RIN n/a n/a
135 1JAN - PRO LEU GLY HOA n/a n/a
136 5H8X ic50 = 3.1 uM 7FY C18 H15 N O4 S c1ccc(cc1)....
137 1MMB - BAT C23 H31 N3 O4 S2 CC(C)C[C@H....
138 3DPF - AXB C24 H21 N5 O6 S2 c1cc2c(cc1....
139 1JJ9 ic50 = 1700 nM BBT C17 H21 N3 O4 c1ccc(cc1)....
140 1ZVX Ki = 0.6 nM FIN C17 H22 N O6 P S CC(C)[C@H]....
141 3TT4 Ki = 5.3 nM E1S C19 H22 N2 O4 S Cc1ccc(s1)....
142 1MMQ Ki = 0.03 uM RRS C25 H36 N4 O4 CC(C)C[C@H....
143 2Y6C ic50 = 0.0001 M TQI C18 H14 Cl F3 N2 O4 S c1ccc2c(c1....
144 1MMP Ki = 0.85 uM RSS C25 H35 N3 O4 CC(C)C[C@H....
145 1MMR Ki = 4 uM SRS C25 H39 N5 O2 S CC(C)C[C@H....
146 4JQG - 8MC PRO LEU GLY PFF DNW ALA ARG NH2 n/a n/a
147 1GKC - NFH C15 H29 N3 O4 CC(C)C[C@H....
148 5I12 ic50 = 1200 nM H27 C34 H42 N4 O12 S2 CC(C)[C@H]....
149 1GKD - STN BUM n/a n/a
150 2OW0 - 6MR C23 H19 I N2 O4 S c1ccc2c(c1....
151 4WZV ic50 = 0.43 nM E40 C28 H29 N3 O8 S CC(C)ON([C....
152 2OVX - 4MR C24 H22 N6 O4 c1ccc(cc1)....
153 6ESM - B9Z C24 H22 O5 S COc1ccc(cc....
154 4JIJ - 8MC PRO LEU GLY PHI DNW ALA ARG NH2 n/a n/a
155 4XCT ic50 = 6.7 nM N73 C20 H24 N2 O5 S CC(C)[C@H]....
156 2OW1 - 7MR C16 H15 F3 N2 O5 S c1ccc(cc1)....
157 2OVZ - 5MR C30 H29 N4 O5 P c1ccc(cc1)....
158 1CGL Ki = 135 nM 0ED C33 H47 N5 O7 NULL
159 966C Ki = 23 nM RS2 C19 H21 N O6 S c1ccc(cc1)....
160 2TCL ic50 = 9 nM RO4 C19 H35 N3 O6 CCOC(=O)[C....
161 1HFC - PLH C18 H27 N3 O4 CC(C)C[C@H....
162 5UE4 Kd = 3.3 uM 5XQ C16 H16 N4 O2 S2 Cc1c(sc(n1....
163 1RM8 - BAT C23 H31 N3 O4 S2 CC(C)C[C@H....
164 1Q3A - NGH C13 H20 N2 O5 S CC(C)C[N@]....
165 5H0U - HIS HIS HIS HIS HIS HIS n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ALA PHE THR SER; Similar ligands found: 41
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA PHE THR SER 1 1
2 ALA PHE THR 0.637681 0.875
3 ALA GLU THR PHE TYR VAL ASP GLY 0.546392 0.72549
4 ARG ILE PHE SER 0.532609 0.711538
5 ASP PHE M3L THR ASP 0.526316 0.633333
6 ALA GLU THR PHE 0.52439 0.840909
7 LEU SER PRO ASP SER PHE LEU ASN ASP 0.512821 0.904762
8 PHE LEU SER THR LYS 0.494737 0.833333
9 PHE SER ALA PTR VAL SER GLU GLU ASP 0.485437 0.727273
10 LEU VAL THR LEU VAL PHE VAL 0.483871 0.880952
11 GLU VAL TYR GLU SER 0.478261 0.791667
12 GLY ILE LEU GLY PHE VAL PHE THR LEU 0.476636 0.795918
13 ACE PHE ALA THR ALA NH2 0.46988 0.902439
14 ASP SER GLY PHE SER PHE GLY SER LYS 0.469136 0.8
15 TYR SER THR CYS TYR PHE ILE MET 0.46729 0.722222
16 GLU THR VAL ARG PHE GLN SER ASP 0.464912 0.754717
17 VAL ALA PHE ARG SER 0.463918 0.72549
18 LYS PHE LYS 0.463415 0.652174
19 SER LEU PHE ASN THR ILE ALA VAL LEU 0.460177 0.851064
20 ALA ALA PHE 0.453333 0.725
21 LYS ALA VAL PHE ASN PHE ALA THR MET 0.45283 0.711538
22 SER LEU PHE ASN THR VAL ALA THR LEU TYR 0.452174 0.8
23 ALA THR ARG ASN PHE SER GLY 0.448598 0.740741
24 TYR GLN GLU SER THR ASP PHE THR PHE LEU 0.446809 0.787234
25 ILE ASN PHE ASP PHE ASN THR ILE 0.443299 0.74
26 THR PHE LYS LYS THR ASN 0.443299 0.78
27 SER GLY ILE PHE LEU GLU THR SER 0.441176 0.833333
28 ACE PHE HIS THR ALA NH2 0.4375 0.711538
29 ACE PHE HIS THR ABA NH2 0.43299 0.698113
30 ASP PHE SER ILE 0.426966 0.866667
31 CYS ASP PTR ALA ASN PHE LYS 0.426966 0.729167
32 ALA TYR ARG 0.422222 0.660377
33 CYS THR PHE LYS THR LYS THR ASN 0.421569 0.764706
34 LYS ALA VAL TYR ASN PHE ALA THR MET 0.421053 0.672727
35 SER PHE ALA ASN GLY 0.419355 0.826087
36 SER LEU PHE ASN THR VAL ALA THR LEU 0.418182 0.869565
37 ALA ILE PHE GLN SER SER MET THR LYS 0.410256 0.727273
38 GLU THR PHE TYR VAL ASP GLY 0.407407 0.735849
39 CYS VAL ASN GLY SER CYS PHE THR VAL 0.40708 0.816327
40 ILE MET ILE SER PHE 0.40404 0.8125
41 ASP ASP ASP MET GLY PHE GLY LEU PHE ASP 0.402062 0.714286
Similar Ligands (3D)
Ligand no: 1; Ligand: ALA PHE THR SER; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4IN9; Ligand: SER TRP PHE PRO; 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: 4in9.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
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