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Receptor
PDB id Resolution Class Description Source Keywords
3B2P 2 Å EC: 3.4.11.2 CRYSTAL STRUCTURE OF E. COLI AMINOPEPTIDASE N IN COMPLEX WIT ESCHERICHIA COLI K12 PROTEASE HYDROLASE AMINOPEPTIDASE N THERMOLYSIN MEMBRANEBINDING METALLOPROTEASE ----
Ref.: STRUCTURAL BASIS FOR THE UNUSUAL SPECIFICITY OF ESC COLI AMINOPEPTIDASE N. BIOCHEMISTRY V. 47 5303 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG A:900;
Valid;
none;
submit data
175.209 C6 H15 N4 O2 C(C[C...
GOL A:970;
A:971;
A:972;
A:973;
A:974;
A:975;
A:976;
A:978;
A:980;
A:981;
A:982;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MLI A:990;
Invalid;
none;
submit data
102.046 C3 H2 O4 C(C(=...
NA A:951;
A:952;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
ZN A:950;
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 (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 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 6G8B - 7MF C17 H19 Br N O2 c1ccc(cc1)....
11 2DQM - BES C16 H24 N2 O4 CC(C)C[C@@....
12 5MFS Ki = 330 nM 7ML C17 H20 N O2 c1ccc(cc1)....
13 3KED ic50 = 3.6 mM DAB C4 H10 N2 O2 C(CN)[C@@H....
14 3QJX - SER C3 H7 N O3 C([C@@H](C....
15 4Q4E ic50 = 0.19 uM BB2 C19 H35 N3 O5 CCCCC[C@H]....
16 3B2P - ARG C6 H15 N4 O2 C(C[C@@H](....
70% Homology Family (16)
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 6G8B - 7MF C17 H19 Br N O2 c1ccc(cc1)....
11 2DQM - BES C16 H24 N2 O4 CC(C)C[C@@....
12 5MFS Ki = 330 nM 7ML C17 H20 N O2 c1ccc(cc1)....
13 3KED ic50 = 3.6 mM DAB C4 H10 N2 O2 C(CN)[C@@H....
14 3QJX - SER C3 H7 N O3 C([C@@H](C....
15 4Q4E ic50 = 0.19 uM BB2 C19 H35 N3 O5 CCCCC[C@H]....
16 3B2P - ARG C6 H15 N4 O2 C(C[C@@H](....
50% Homology Family (52)
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 6G8B - 7MF C17 H19 Br N O2 c1ccc(cc1)....
11 2DQM - BES C16 H24 N2 O4 CC(C)C[C@@....
12 5MFS Ki = 330 nM 7ML C17 H20 N O2 c1ccc(cc1)....
13 3KED ic50 = 3.6 mM DAB C4 H10 N2 O2 C(CN)[C@@H....
14 3QJX - SER C3 H7 N O3 C([C@@H](C....
15 4Q4E ic50 = 0.19 uM BB2 C19 H35 N3 O5 CCCCC[C@H]....
16 3B2P - ARG C6 H15 N4 O2 C(C[C@@H](....
17 6EA1 Ki = 331 nM J0Y C17 H11 F7 N2 O3 c1cc(ccc1c....
18 4K5N Ki = 127 uM 1OU C8 H13 N4 O3 P [H]/N=C(/N....
19 4R5T Ki = 0.8 uM R5T C16 H20 N4 O4 CC(C)(C)OC....
20 4ZX6 Ki = 5.4 uM 4U6 C20 H24 N4 O4 CC(C)(C)C(....
21 4K5P Ki = 345 uM 1OS C8 H12 N3 O3 P [H]/N=C(c1....
22 6EAB Ki = 431 nM J2D C20 H19 F3 N2 O4 c1cc(ccc1c....
23 4ZX5 Ki = 0.64 uM 4TM C17 H20 N2 O3 S CC(C)(C)C(....
24 3EBH Ki = 478.2 nM BES C16 H24 N2 O4 CC(C)C[C@@....
25 6EE4 Ki = 202 nM J4S C19 H17 F3 N2 O3 c1cc(ccc1c....
26 4ZX4 Ki = 0.078 uM 4TL C19 H19 F3 N2 O3 CC(C)(C)C(....
27 4ZW7 Ki = 19 uM 4SZ C19 H19 F3 N2 O4 CC(C)(C)OC....
28 4ZW3 Ki = 0.027 uM 4S9 C13 H17 Br N2 O4 CC(C)(C)OC....
29 6EED Ki = 812 nM J6A C22 H23 F3 N2 O3 c1cc(ccc1c....
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 6EE3 Ki = 137 nM J4V C25 H25 F3 N2 O3 c1cc(ccc1c....
35 3Q43 Ki = 43 nM D66 C17 H26 N2 O5 CC(C)C[C@@....
36 4ZW5 Ki = 37 uM 4SA C19 H22 N2 O4 CC(C)(C)OC....
37 4X2U - TOD C16 H22 N2 O6 CC(C)C[C@H....
38 6EE6 Ki = 216 nM J4P C21 H21 F3 N2 O3 c1cc(ccc1c....
39 3T8V Ki = 260 nM BTJ C54 H67 N7 O11 C[C@@H](C(....
40 4K5O Ki = 104 uM 1OT C10 H12 N3 O3 P c1cnn(c1)c....
41 4R5X Ki = 5.5 uM R5X C18 H17 N5 O3 c1cc(cc(c1....
42 6EA2 Ki = 285 nM J1G C20 H19 F3 N2 O3 c1cc(ccc1c....
43 3EBI Ki = 79 nM BEY C19 H24 N O4 P c1ccc(cc1)....
44 4ZW6 Ki = 1.9 uM 4SY C17 H22 N4 O4 CC(C)(C)OC....
45 6EAA Ki = 818 nM J1V C21 H21 F3 N2 O3 c1cc(ccc1c....
46 4R5V Ki = 0.7 uM R5V C16 H20 N4 O3 CC(C)(C)C(....
47 4K5L Ki = 11 uM 19N C6 H17 N4 O3 P [H]/N=C(N)....
48 4QHP Ki = 9 nM 32Q C20 H27 N2 O4 P c1ccc(cc1)....
49 4QIR Ki = 112 nM 379 C18 H23 N2 O4 P c1ccc(cc1)....
50 4QUO Ki = 12 nM 3DZ C20 H27 N2 O4 P c1ccc(cc1)....
51 4QPE - 37E C8 H19 N2 O3 P C1CCC(CC1)....
52 4QME Ki = 302 nM 37B C19 H24 N O4 P c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG; Similar ligands found: 42
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG 1 1
2 DAR 1 1
3 CIR 0.735294 0.763158
4 AAR 0.705882 0.783784
5 ILO 0.615385 0.783784
6 3AR 0.595238 0.891892
7 4JK 0.585366 0.789474
8 NMM 0.585366 0.888889
9 VUR 0.585366 0.810811
10 HAR 0.585366 0.780488
11 VIO 0.581395 0.769231
12 WT2 0.571429 0.805556
13 DA2 0.55814 0.744186
14 2MR 0.545455 0.864865
15 2YH 0.545455 0.65
16 3KJ 0.545455 0.680851
17 1KJ 0.533333 0.744186
18 JM2 0.533333 0.731707
19 NRG 0.521739 0.622642
20 RPI 0.521739 0.64
21 2YJ 0.521739 0.619048
22 API 0.515152 0.611111
23 LN6 0.510638 0.725
24 HRG 0.5 0.941176
25 JM7 0.5 0.731707
26 2KJ 0.489796 0.727273
27 D20 0.489796 0.744186
28 AS1 0.489796 0.8
29 ORN 0.472222 0.757576
30 JM8 0.470588 0.714286
31 JM6 0.470588 0.697674
32 JM4 0.470588 0.697674
33 LYS ARG LYS ARG LYS ARG LYS ARG 0.463415 0.848485
34 MLZ 0.463415 0.65
35 JM5 0.461538 0.714286
36 DLY 0.447368 0.735294
37 DAB 0.441176 0.685714
38 LYS 0.435897 0.764706
39 0TF 0.428571 0.619048
40 2YG 0.42 0.619048
41 PG3 0.416667 0.756757
42 6CL 0.414634 0.638889
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2ZXG; Ligand: S23; Similar sites found with APoc: 150
This union binding pocket(no: 1) in the query (biounit: 2zxg.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 5A3Y VAL LYS 1.45985
2 5CX6 CDP 1.70213
3 3O01 DXC 1.94805
4 3AHO 3A2 1.95035
5 4MRP GSH 1.9544
6 3FXU TSU 1.96721
7 5KDS A2G THR ALA PRO GLY GLY NAG SIA 2.07547
8 4U60 SIA 2.14286
9 3HBV ALA LYS ALA SER GLN ALA ALA 2.1645
10 3B9Z CO2 2.31959
11 2GWH PCI 2.34899
12 1VAY AZA 2.43902
13 3ETG GTP 2.59481
14 5VRH OLB 2.68199
15 4V3I ASP LEU THR ARG PRO 2.72374
16 5OSW DIU 2.74443
17 2YP9 SIA CMO 2.7833
18 5O7E 9NB 2.79898
19 3S5W ONH 2.80778
20 2EA1 GPG 2.85714
21 1XF1 CIT 2.87356
22 4CA5 3EF 2.88625
23 5JF2 SF7 2.94118
24 4Z87 GDP 3.04762
25 2J83 BAT 3.05344
26 1Y79 LYS TRP 3.08824
27 3M6P BB2 3.10881
28 4DR9 BB2 3.125
29 4CME KTZ 3.125
30 5OKT 9XK 3.18471
31 2GBB CIT 3.20513
32 1FUI FOC 3.21489
33 5MZI FYK 3.2538
34 1YKD CMP 3.26633
35 3G5K BB2 3.27869
36 5L44 K26 3.3675
37 2J4D MHF 3.42857
38 2YIV YIV 3.5061
39 3WV1 WHH 3.50877
40 3E3U NVC 3.5533
41 4BXK 1IU 3.6566
42 1ZED PNP 3.71901
43 4TVD BGC 3.7931
44 3UWB BB2 3.8961
45 5X3R 7Y3 3.90244
46 5M37 9SZ 3.91304
47 3RET SAL 3.9604
48 3RET PYR 3.9604
49 1VBO MAN 4.02685
50 4XNV BUR 4.038
51 1FBL HTA 4.05405
52 4K90 MLA 4.18605
53 3HW5 AMP 4.21456
54 3D3X ARG ILE MET GLU NH2 4.21546
55 5L7V GNL 4.26288
56 1R6N 434 4.2654
57 3DWB RDF 4.32836
58 2NUN ADP 4.33437
59 3C88 ARG ARG GLY CYS NH2 4.39815
60 2NV2 GLN 4.42177
61 1YP1 LYS ASN LEU 4.45545
62 6BTN E8M 4.45545
63 6BTQ E8S 4.45545
64 4DV8 0LX 4.56274
65 4AR8 IP8 GLY PRO ALA 4.56853
66 5L8N 6RQ 4.6875
67 1MMQ RRS 4.70588
68 2YB9 HA0 4.74138
69 5AMC GLY NIY 4.76948
70 4EOX 0S5 4.92611
71 1ATL 0QI 4.9505
72 2FV5 541 4.98084
73 6H8S FSZ 4.98339
74 1BKC INN 5.07812
75 3CQO FUC 5.11945
76 5UGW GSH 5.14286
77 5KD8 TNR 5.18784
78 3ZQE DXC 5.2459
79 1RL4 BRR 5.31915
80 3Q2H QHF 5.38721
81 2OKL BB2 5.40541
82 2W14 WR2 5.44554
83 2V57 PRL 5.78947
84 5H0U HIS HIS HIS HIS HIS HIS 5.88235
85 4WKI 3PW 5.95745
86 4TV1 36M 5.9761
87 1QJI PKF 6
88 1Q1Y BB2 6.28272
89 1R55 097 6.54206
90 5A0R ACE GLU VAL ASN PRO 6.56566
91 5A4W QCT 6.60377
92 3KP6 SAL 6.62252
93 4IN9 SER TRP PHE PRO 6.62651
94 2TCL RO4 7.10059
95 1NU4 MLA 7.2165
96 4B52 RDF 7.23684
97 5MTE BB2 7.29927
98 4DO1 ANN 7.31707
99 3UEC ALA ARG TPO LYS 7.53425
100 5KDX GAL TNR 7.58621
101 1G27 BB1 7.7381
102 6CEP OXM 7.78443
103 1KUK PCA LYS TRP 7.88177
104 1M2X MCO 8.07175
105 1RM8 BAT 8.28402
106 2ZQO NGA 8.46154
107 3KO0 TFP 8.91089
108 2VWA PTY 8.91089
109 1KAP GLY SER ASN SER 9.1858
110 5CHR 4NC 9.48905
111 3N7S 3N7 9.56522
112 1Q3A NGH 9.69697
113 3HYW DCQ 9.76744
114 4TMN 0PK 9.81013
115 3ZVS MLI 10
116 1HFS L04 10
117 2OUA AES 10.1064
118 1LQY BB2 10.3261
119 5W7B MYR 10.6383
120 3TL1 JRO 10.6918
121 4DD8 BAT 11.0577
122 4KJU 1RH 11.6279
123 1ECM TSA 12.844
124 5V4R MGT 12.963
125 5HWV MBN 13.0769
126 5M36 9SZ 13.1579
127 5F5N 5VD 13.4948
128 5NNT DPV 13.5135
129 4WZV E40 13.75
130 1S17 GNR 13.8889
131 4AIG FLX 14.4279
132 1ZVX FIN 14.7239
133 5LX9 OLB 17.2638
134 4KX8 L2O VAL VAL ASP 17.5862
135 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 17.931
136 1WS1 BB2 17.9487
137 6GMN F4E 18.2692
138 5LWY OLB 20.1681
139 5C9J DAO 20.202
140 1XXA ARG 21.7949
141 2VJ8 HA2 25.0409
142 4JE7 BB2 26.9036
143 2Y69 CHD 28.75
144 4RJD TFP 28.7879
145 2XQ0 BES 28.9557
146 4GAA BES 33.0049
147 4OGQ 7PH 40.5405
148 5Z84 CHD 41.0714
149 5ZCO CHD 41.0714
150 5W97 CHD 41.0714
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