Receptor
PDB id Resolution Class Description Source Keywords
3QJX 1.45 Å EC: 3.4.11.2 CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX WIT ESCHERICHIA COLI THERMOLYSIN LIKE CATALYTIC DOMAIN HYDROLASE L-SERINE COMPL
Ref.: DISCOVERY OF ALPHA, BETA- AND ALPHA, GAMMA-DIAMINO SCAFFOLDS FOR THE INHIBITION OF M1 FAMILY AMINOPEPT CHEMMEDCHEM V. 6 1971 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:970;
A:971;
A:972;
A:973;
A:974;
A:975;
A:976;
A:977;
A:978;
A:979;
A:981;
A:982;
A:983;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MLI A:950;
Invalid;
none;
submit data
102.046 C3 H2 O4 C(C(=...
NA A:890;
A:891;
A:892;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
22.99 Na [Na+]
SER A:900;
Valid;
none;
submit data
105.093 C3 H7 N O3 C([C@...
ZN A:880;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2ZXG 1.55 Å EC: 3.4.11.2 AMINOPEPTIDASE N COMPLEXED WITH THE AMINOPHOSPHINIC INHIBITO PL250, A TRANSITION STATE ANALOGUE ESCHERICHIA COLI K-12 CLAN MA FAMILY M1 ZINC PEPTIDASE INHIBITOR COMPLEX TRANSSTATE AMINOPEPTIDASE CELL INNER MEMBRANE CELL MEMBRANE HYDROLASE MEMBRANE METAL-BINDING METALLOPROTEASE PROTEA
Ref.: STRUCTURE OF AMINOPEPTIDASE N FROM ESCHERICHIA COLI COMPLEXED WITH THE TRANSITION-STATE ANALOGUE AMINOP INHIBITOR PL250 ACTA CRYSTALLOGR.,SECT.D V. 65 814 2009
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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](....
70% Homology Family (15)
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](....
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: SER; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 SER 1 1
2 DSN 1 1
3 DCY 0.65 0.84
4 CYS 0.65 0.84
5 ABA 0.6 0.692308
6 DBB 0.6 0.692308
7 2RA 0.6 0.75
8 HSE 0.590909 0.821429
9 C2N 0.571429 0.730769
10 ASN 0.545455 0.625
11 ASP 0.545455 0.714286
12 DAS 0.545455 0.714286
13 DAB 0.521739 0.724138
14 AS2 0.5 0.703704
15 LEU 0.5 0.642857
16 HCS 0.5 0.777778
17 NVA 0.5 0.62069
18 CSO 0.5 0.636364
19 API 0.5 0.633333
20 CSS 0.48 0.689655
21 DGY 0.47619 0.607143
22 DGL 0.461538 0.655172
23 GLU 0.461538 0.655172
24 GGL 0.461538 0.655172
25 ORN 0.444444 0.689655
26 SLZ 0.433333 0.625
27 UN1 0.413793 0.633333
28 DLY 0.413793 0.666667
29 11C 0.413793 0.633333
30 CME 0.40625 0.666667
31 DHH 0.4 0.612903
32 LYS 0.4 0.645161
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2ZXG; Ligand: S23; Similar sites found: 88
This union binding pocket(no: 1) in the query (biounit: 2zxg.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A3Y VAL LYS 0.01391 0.42427 1.45985
2 5CX6 CDP 0.02437 0.41243 1.70213
3 3AHO 3A2 0.001079 0.42785 1.95035
4 4MRP GSH 0.04276 0.41231 1.9544
5 5KDS A2G THR ALA PRO GLY GLY NAG SIA 0.006889 0.41762 2.07547
6 4U60 SIA 0.04992 0.40002 2.14286
7 1VAY AZA 0.03457 0.40407 2.43902
8 4V3I ASP LEU THR ARG PRO 0.02321 0.41403 2.72374
9 4ARF IP8 GLY PRO ALA 0.001132 0.43905 2.79188
10 3S5W ONH 0.01334 0.4227 2.80778
11 5JF2 SF7 0.001162 0.44489 2.94118
12 2J83 BAT 0.000792 0.44813 3.05344
13 1Y79 LYS TRP 0.00002149 0.5619 3.08824
14 1Y79 GLY ASP 0.009071 0.45089 3.08824
15 3M6P BB2 0.000227 0.4163 3.10881
16 4DR9 BB2 0.00008422 0.50624 3.125
17 2GBB CIT 0.008637 0.42934 3.20513
18 1FUI FOC 0.02908 0.40715 3.21489
19 3G5K BB2 0.0002435 0.4849 3.27869
20 5L44 K26 0.0002821 0.48194 3.3675
21 2J4D MHF 0.03313 0.40333 3.42857
22 3WV1 WHH 0.001693 0.43616 3.50877
23 3E3U NVC 0.00004464 0.52513 3.5533
24 3UWB BB2 0.004192 0.41012 3.8961
25 3RET SAL 0.01131 0.41121 3.9604
26 3RET PYR 0.01131 0.41121 3.9604
27 1VBO MAN 0.04889 0.40362 4.02685
28 4XNV BUR 0.01017 0.43335 4.038
29 4K90 MLA 0.003861 0.45451 4.18605
30 3HW5 AMP 0.02065 0.41672 4.21456
31 3D3X ARG ILE MET GLU NH2 0.00472 0.40797 4.21546
32 5L7V GNL 0.03063 0.40514 4.26288
33 3DWB RDF 0.0006 0.47692 4.32836
34 2NUN ADP 0.02744 0.40359 4.33437
35 4DV8 0LX 0.0001517 0.47116 4.56274
36 4AR8 IP8 GLY PRO ALA 0.000002048 0.58097 4.56853
37 5L8N 6RQ 0.03377 0.40308 4.6875
38 1MMQ RRS 0.00008189 0.50127 4.70588
39 5AMC GLY NIY 0.005854 0.43796 4.76948
40 1ATL 0QI 0.00007184 0.45467 4.9505
41 2FV5 541 0.0009231 0.40638 4.98084
42 1BKC INN 0.0001333 0.40645 5.07812
43 5UGW GSH 0.01101 0.41211 5.14286
44 1RL4 BRR 0.000509 0.49838 5.31915
45 3Q2H QHF 0.0007463 0.45342 5.38721
46 2OKL BB2 0.0009038 0.45401 5.40541
47 2W14 WR2 0.000156 0.40736 5.44554
48 3DBK RDF 0.0005036 0.40855 5.64784
49 2V57 PRL 0.01883 0.4188 5.78947
50 4WKI 3PW 0.0002423 0.496 5.95745
51 4TV1 36M 0.02218 0.41256 5.9761
52 1QJI PKF 0.004385 0.42673 6
53 1Q1Y BB2 0.0004745 0.47652 6.28272
54 1R55 097 0.0003012 0.50357 6.54206
55 5A0R ACE GLU VAL ASN PRO 0.002479 0.41187 6.56566
56 4IN9 SER TRP PHE PRO 0.0008524 0.48957 6.62651
57 2TCL RO4 0.0001561 0.43378 7.10059
58 1NU4 MLA 0.03181 0.4207 7.2165
59 4B52 RDF 0.0002766 0.40266 7.23684
60 4DO1 ANN 0.04149 0.40274 7.31707
61 5KDX GAL TNR 0.004509 0.45331 7.58621
62 1G27 BB1 0.0001548 0.48372 7.7381
63 3KO0 TFP 0.01107 0.4302 8.91089
64 2VWA PTY 0.02933 0.40607 8.91089
65 5CHR 4NC 0.03393 0.40418 9.48905
66 3N7S 3N7 0.01435 0.4271 9.56522
67 1Q3A NGH 0.00005887 0.40443 9.69697
68 3HYW DCQ 0.03051 0.40732 9.76744
69 4TMN 0PK 0.001431 0.42622 9.81013
70 3SVJ 4LI 0.001441 0.40209 9.85222
71 3ZVS MLI 0.00005263 0.53193 10
72 2OUA AES 0.01541 0.42603 10.1064
73 1LQY BB2 0.0003327 0.47368 10.3261
74 3TL1 JRO 0.01927 0.41578 10.6918
75 4DD8 BAT 0.0002772 0.51215 11.0577
76 4KJU 1RH 0.03143 0.40964 11.6279
77 1ECM TSA 0.01619 0.41537 12.844
78 5V4R MGT 0.001518 0.46995 12.963
79 5F5N 5VD 0.02164 0.40125 13.4948
80 4WZV E40 0.0002227 0.45544 13.75
81 1S17 GNR 0.0002535 0.47422 13.8889
82 3HY9 098 0.0009167 0.44945 15.3846
83 4KX8 L2O VAL VAL ASP 0.000000001096 0.70277 17.5862
84 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 0.00000005263 0.53237 17.931
85 1WS1 BB2 0.0001095 0.50097 17.9487
86 2VJ8 HA2 0.0000001205 0.48095 25.0409
87 2XQ0 BES 0.000000009374 0.50835 28.9557
88 4GAA BES 0.000000003526 0.70894 33.0049
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