Receptor
PDB id Resolution Class Description Source Keywords
4ZW3 1.8 Å EC: 3.4.11.- X-RAY CRYSTAL STRUCTURE OF PFA-M1 IN COMPLEX WITH HYDROXAMIC BASED INHIBITOR 9B PLASMODIUM FALCIPARUM (ISOLATE FCB1 / COLUMBIA) M1 ALANYL-AMINOPEPTIDASE PROTEASE INHIBITOR HYDROXAMIC ACHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: POTENT DUAL INHIBITORS OF PLASMODIUM FALCIPARUM M1 AMINOPEPTIDASES THROUGH OPTIMIZATION OF S1 POCKET INTERACTIONS. EUR.J.MED.CHEM. V. 110 43 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1104;
A:1103;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
ZN A:1102;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
4S9 A:1101;
 Valid;
 none;
 Ki = 0.027 uM
345.189 C13 H17 Br N2 O4 CC(C)...
PO4 A:1106;
 Invalid;
 none;
 submit data
94.971 O4 P [O-]P...
MG A:1105;
 Invalid;
 none;
 submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4ZW3 1.8 Å EC: 3.4.11.- X-RAY CRYSTAL STRUCTURE OF PFA-M1 IN COMPLEX WITH HYDROXAMIC BASED INHIBITOR 9B PLASMODIUM FALCIPARUM (ISOLATE FCB1 / COLUMBIA) M1 ALANYL-AMINOPEPTIDASE PROTEASE INHIBITOR HYDROXAMIC ACHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: POTENT DUAL INHIBITORS OF PLASMODIUM FALCIPARUM M1 AMINOPEPTIDASES THROUGH OPTIMIZATION OF S1 POCKET INTERACTIONS. EUR.J.MED.CHEM. V. 110 43 2016
Members (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4K5N Ki = 127 uM 1OU C8 H13 N4 O3 P [H]/N=C(/N....
2 4R5T Ki = 0.8 uM R5T C16 H20 N4 O4 CC(C)(C)OC....
3 4ZX6 Ki = 5.4 uM 4U6 C20 H24 N4 O4 CC(C)(C)C(....
4 4K5P Ki = 345 uM 1OS C8 H12 N3 O3 P [H]/N=C(c1....
5 4ZX5 Ki = 0.64 uM 4TM C17 H20 N2 O3 S CC(C)(C)C(....
6 3EBH Ki = 478.2 nM BES C16 H24 N2 O4 CC(C)C[C@@....
7 4ZX4 Ki = 0.078 uM 4TL C19 H19 F3 N2 O3 CC(C)(C)C(....
8 4ZW7 Ki = 19 uM 4SZ C19 H19 F3 N2 O4 CC(C)(C)OC....
9 4ZW3 Ki = 0.027 uM 4S9 C13 H17 Br N2 O4 CC(C)(C)OC....
10 4K5M Ki = 193 uM 1OV C5 H15 N4 O3 P [H]/N=C(/N....
11 4ZW8 Ki = 1.1 uM 4T2 C20 H24 N4 O5 CC(C)(C)OC....
12 4ZX3 Ki = 0.065 uM 4TK C13 H17 Br N2 O3 CC(C)(C)C(....
13 3Q44 Ki = 490 nM D50 C23 H30 N2 O5 CC(C)C[C@@....
14 3Q43 Ki = 43 nM D66 C17 H26 N2 O5 CC(C)C[C@@....
15 4ZW5 Ki = 37 uM 4SA C19 H22 N2 O4 CC(C)(C)OC....
16 4X2U - TOD C16 H22 N2 O6 CC(C)C[C@H....
17 3T8V Ki = 260 nM BTJ C54 H67 N7 O11 C[C@@H](C(....
18 4K5O Ki = 104 uM 1OT C10 H12 N3 O3 P c1cnn(c1)c....
19 4R5X Ki = 5.5 uM R5X C18 H17 N5 O3 c1cc(cc(c1....
20 3EBI Ki = 79 nM BEY C19 H24 N O4 P c1ccc(cc1)....
21 4ZW6 Ki = 1.9 uM 4SY C17 H22 N4 O4 CC(C)(C)OC....
22 4R5V Ki = 0.7 uM R5V C16 H20 N4 O3 CC(C)(C)C(....
23 4K5L Ki = 11 uM 19N C6 H17 N4 O3 P [H]/N=C(N)....
70% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4K5N Ki = 127 uM 1OU C8 H13 N4 O3 P [H]/N=C(/N....
2 4R5T Ki = 0.8 uM R5T C16 H20 N4 O4 CC(C)(C)OC....
3 4ZX6 Ki = 5.4 uM 4U6 C20 H24 N4 O4 CC(C)(C)C(....
4 4K5P Ki = 345 uM 1OS C8 H12 N3 O3 P [H]/N=C(c1....
5 4ZX5 Ki = 0.64 uM 4TM C17 H20 N2 O3 S CC(C)(C)C(....
6 3EBH Ki = 478.2 nM BES C16 H24 N2 O4 CC(C)C[C@@....
7 4ZX4 Ki = 0.078 uM 4TL C19 H19 F3 N2 O3 CC(C)(C)C(....
8 4ZW7 Ki = 19 uM 4SZ C19 H19 F3 N2 O4 CC(C)(C)OC....
9 4ZW3 Ki = 0.027 uM 4S9 C13 H17 Br N2 O4 CC(C)(C)OC....
10 4K5M Ki = 193 uM 1OV C5 H15 N4 O3 P [H]/N=C(/N....
11 4ZW8 Ki = 1.1 uM 4T2 C20 H24 N4 O5 CC(C)(C)OC....
12 4ZX3 Ki = 0.065 uM 4TK C13 H17 Br N2 O3 CC(C)(C)C(....
13 3Q44 Ki = 490 nM D50 C23 H30 N2 O5 CC(C)C[C@@....
14 3Q43 Ki = 43 nM D66 C17 H26 N2 O5 CC(C)C[C@@....
15 4ZW5 Ki = 37 uM 4SA C19 H22 N2 O4 CC(C)(C)OC....
16 4X2U - TOD C16 H22 N2 O6 CC(C)C[C@H....
17 3T8V Ki = 260 nM BTJ C54 H67 N7 O11 C[C@@H](C(....
18 4K5O Ki = 104 uM 1OT C10 H12 N3 O3 P c1cnn(c1)c....
19 4R5X Ki = 5.5 uM R5X C18 H17 N5 O3 c1cc(cc(c1....
20 3EBI Ki = 79 nM BEY C19 H24 N O4 P c1ccc(cc1)....
21 4ZW6 Ki = 1.9 uM 4SY C17 H22 N4 O4 CC(C)(C)OC....
22 4R5V Ki = 0.7 uM R5V C16 H20 N4 O3 CC(C)(C)C(....
23 4K5L Ki = 11 uM 19N C6 H17 N4 O3 P [H]/N=C(N)....
50% Homology Family (43)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5MFT Ki = 34 nM 7MF C17 H19 Br N O2 c1ccc(cc1)....
2 3B3B - TRP C11 H12 N2 O2 c1ccc2c(c1....
3 3B2X - LYS C6 H15 N2 O2 C(CC[NH3+]....
4 4Q4I ic50 = 0.047 uM L2O VAL VAL ASP n/a n/a
5 5MFR Ki = 50000 nM 7MK C11 H16 N O2 c1ccc2c(c1....
6 3B34 - PHE C9 H11 N O2 c1ccc(cc1)....
7 2ZXG Ki = 15 nM S23 C21 H27 N2 O5 P C[C@H](N)[....
8 3B37 - TYR C9 H11 N O3 c1cc(ccc1C....
9 2HPT - BES C16 H24 N2 O4 CC(C)C[C@@....
10 2DQM - BES C16 H24 N2 O4 CC(C)C[C@@....
11 5MFS Ki = 330 nM 7ML C17 H20 N O2 c1ccc(cc1)....
12 3KED ic50 = 3.6 mM DAB C4 H10 N2 O2 C(CN)[C@@H....
13 3QJX - SER C3 H7 N O3 C([C@@H](C....
14 4Q4E ic50 = 0.19 uM BB2 C19 H35 N3 O5 CCCCC[C@H]....
15 3B2P - ARG C6 H15 N4 O2 C(C[C@@H](....
16 4QHP Ki = 9 nM 32Q C20 H27 N2 O4 P c1ccc(cc1)....
17 4QIR Ki = 112 nM 379 C18 H23 N2 O4 P c1ccc(cc1)....
18 4QUO Ki = 12 nM 3DZ C20 H27 N2 O4 P c1ccc(cc1)....
19 4QPE - 37E C8 H19 N2 O3 P C1CCC(CC1)....
20 4QME Ki = 302 nM 37B C19 H24 N O4 P c1ccc(cc1)....
21 4K5N Ki = 127 uM 1OU C8 H13 N4 O3 P [H]/N=C(/N....
22 4R5T Ki = 0.8 uM R5T C16 H20 N4 O4 CC(C)(C)OC....
23 4ZX6 Ki = 5.4 uM 4U6 C20 H24 N4 O4 CC(C)(C)C(....
24 4K5P Ki = 345 uM 1OS C8 H12 N3 O3 P [H]/N=C(c1....
25 4ZX5 Ki = 0.64 uM 4TM C17 H20 N2 O3 S CC(C)(C)C(....
26 3EBH Ki = 478.2 nM BES C16 H24 N2 O4 CC(C)C[C@@....
27 4ZX4 Ki = 0.078 uM 4TL C19 H19 F3 N2 O3 CC(C)(C)C(....
28 4ZW7 Ki = 19 uM 4SZ C19 H19 F3 N2 O4 CC(C)(C)OC....
29 4ZW3 Ki = 0.027 uM 4S9 C13 H17 Br N2 O4 CC(C)(C)OC....
30 4K5M Ki = 193 uM 1OV C5 H15 N4 O3 P [H]/N=C(/N....
31 4ZW8 Ki = 1.1 uM 4T2 C20 H24 N4 O5 CC(C)(C)OC....
32 4ZX3 Ki = 0.065 uM 4TK C13 H17 Br N2 O3 CC(C)(C)C(....
33 3Q44 Ki = 490 nM D50 C23 H30 N2 O5 CC(C)C[C@@....
34 3Q43 Ki = 43 nM D66 C17 H26 N2 O5 CC(C)C[C@@....
35 4ZW5 Ki = 37 uM 4SA C19 H22 N2 O4 CC(C)(C)OC....
36 4X2U - TOD C16 H22 N2 O6 CC(C)C[C@H....
37 3T8V Ki = 260 nM BTJ C54 H67 N7 O11 C[C@@H](C(....
38 4K5O Ki = 104 uM 1OT C10 H12 N3 O3 P c1cnn(c1)c....
39 4R5X Ki = 5.5 uM R5X C18 H17 N5 O3 c1cc(cc(c1....
40 3EBI Ki = 79 nM BEY C19 H24 N O4 P c1ccc(cc1)....
41 4ZW6 Ki = 1.9 uM 4SY C17 H22 N4 O4 CC(C)(C)OC....
42 4R5V Ki = 0.7 uM R5V C16 H20 N4 O3 CC(C)(C)C(....
43 4K5L Ki = 11 uM 19N C6 H17 N4 O3 P [H]/N=C(N)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4S9; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 4S9 1 1
2 4SA 0.637931 0.849057
3 4TK 0.622642 0.86
4 R5T 0.59375 0.69697
5 4SZ 0.587302 0.875
6 4SY 0.569231 0.707692
7 4T2 0.506849 0.762712
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4ZW3; Ligand: 4S9; Similar sites found: 89
This union binding pocket(no: 1) in the query (biounit: 4zw3.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5KDX GAL TNR 0.01029 0.44536 1.01695
2 5FJJ MAN 0.01365 0.43132 1.30641
3 4FDU IHS 0.03111 0.41021 1.64319
4 2BP1 FLC 0.04966 0.40454 1.66667
5 3R9V DXC 0.03916 0.41123 2.0979
6 4WKI 3PW 0.0002638 0.50675 2.12766
7 4COL DTP 0.02289 0.40295 2.15054
8 5FR0 SIZ 0.02799 0.40528 2.29508
9 1Y79 LYS TRP 0.00003239 0.56674 2.47191
10 1Y79 GLY ASP 0.0106 0.45774 2.47191
11 5AMC GLY NIY 0.004824 0.4529 2.54372
12 1YKD CMP 0.01964 0.40298 2.76382
13 3G58 988 0.02052 0.41582 3.41207
14 4TMN 0PK 0.004507 0.41646 3.48101
15 4I90 CHT 0.02724 0.42071 3.63036
16 5V4R MGT 0.0005759 0.51097 3.70787
17 4ARF IP8 GLY PRO ALA 0.0006294 0.40919 3.80711
18 3G5K BB2 0.0003344 0.4909 3.82514
19 3O01 DXC 0.001098 0.48336 3.8961
20 3UWB BB2 0.007927 0.40885 3.8961
21 1BKC INN 0.00009319 0.52931 3.90625
22 1XMY ROL 0.03668 0.4064 4.0201
23 3E3U NVC 0.00003693 0.54283 4.06091
24 4JE7 BB2 0.00969 0.41413 4.06091
25 1G27 BB1 0.0001783 0.49379 4.16667
26 2FV5 541 0.0004906 0.43741 4.21456
27 1UWC FER 0.02962 0.40402 4.21456
28 1RL4 BRR 0.00152 0.48496 4.25532
29 3DBK RDF 0.002153 0.44416 4.31894
30 3BFV ADP 0.03463 0.40404 4.42804
31 1S17 GNR 0.0002663 0.4858 4.44444
32 3DWB RDF 0.002953 0.45433 4.47761
33 1M48 FRG 0.02815 0.41658 4.51128
34 4X1Z FUC GAL NDG 0.02996 0.4134 4.51807
35 5UGW GSH 0.0185 0.40019 4.57143
36 3D3X ARG ILE MET GLU NH2 0.00646 0.41271 4.68384
37 1MMQ RRS 0.0003924 0.48271 4.70588
38 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.04129 0.40006 4.7619
39 3AHO 3A2 0.0004654 0.45473 4.96454
40 3ZVS MLI 0.0002405 0.50651 5
41 1R55 097 0.0005018 0.50441 5.14019
42 5K53 STE 0.01217 0.40651 5.34351
43 4UCC ZKW 0.025 0.41846 5.5794
44 1WS1 BB2 0.00008274 0.51989 5.76923
45 2V57 PRL 0.008924 0.44476 5.78947
46 4V3I ASP LEU THR ARG PRO 0.001228 0.49177 5.83658
47 2TCL RO4 0.001068 0.45411 5.91716
48 1GG6 APL 0.008762 0.42279 6.18557
49 3OZV ECN 0.01137 0.42118 6.20347
50 4WZV E40 0.001828 0.42992 6.25
51 5GZZ GSH 0.03022 0.41687 6.42202
52 2W14 WR2 0.0003478 0.49527 6.43564
53 3HBV ALA LYS ALA SER GLN ALA ALA 0.0005366 0.49134 6.49351
54 4K90 MLA 0.01053 0.44775 6.51163
55 3AQT RCO 0.04125 0.40902 6.53061
56 4IN9 SER TRP PHE PRO 0.003822 0.46189 6.62651
57 4DR9 BB2 0.00005917 0.52685 6.77083
58 2J83 BAT 0.001315 0.45005 6.87023
59 1QJI PKF 0.01852 0.40739 7
60 4RHS SIA SIA GAL 0.03897 0.40287 7.37705
61 2GBB CIT 0.01134 0.43339 8.33333
62 4DV8 0LX 0.0004416 0.42777 8.36502
63 3N7S 3N7 0.01366 0.43915 8.69565
64 1LQY BB2 0.0001455 0.50288 9.23913
65 5DCH 1YO 0.0426 0.40843 9.375
66 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 0.03403 0.41662 9.56522
67 1Q1Y BB2 0.0004432 0.49013 9.94764
68 1RM8 BAT 0.0005397 0.50912 10.0592
69 5N18 8HZ 0.02697 0.41443 10.0917
70 3HY9 098 0.0003136 0.48255 10.4072
71 5A0R ACE GLU VAL ASN PRO 0.005809 0.40358 10.6061
72 5KD8 TNR 0.003373 0.46635 10.9123
73 3Q2H QHF 0.0001713 0.49459 11.1111
74 2VWA PTY 0.02174 0.42556 11.8812
75 1YP1 LYS ASN LEU 0.0002341 0.5286 12.3762
76 5JF2 SF7 0.0006869 0.46693 12.7451
77 5L44 K26 0.0006944 0.47573 13.1772
78 2OKL BB2 0.0003477 0.48517 13.5135
79 4DS8 A8S 0.01791 0.41148 13.9942
80 1Q3A NGH 0.0003611 0.5119 14.5455
81 5CHR 4NC 0.01803 0.42877 15.3285
82 5KDS A2G THR ALA PRO GLY GLY NAG SIA 0.01364 0.41378 15.6604
83 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 0.0000005568 0.53642 15.7303
84 4DD8 BAT 0.0003116 0.52193 15.8654
85 4KX8 L2O VAL VAL ASP 0.00000001265 0.67559 17.7928
86 4AR8 IP8 GLY PRO ALA 0.000002388 0.59347 19.0355
87 2XQ0 BES 0.00000004729 0.43772 20.0949
88 2VJ8 HA2 0.0000003883 0.50591 31.0966
89 4GAA BES 0.00000001267 0.70221 31.5271
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