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Receptor
PDB id Resolution Class Description Source Keywords
4QHP 1.6 Å EC: 3.4.11.2 CRYSTAL STRUCTURE OF AMINOPEPTIDASE N IN COMPLEX WITH THE PH DIPEPTIDE ANALOGUE LL-(R,S)-HPHEP[CH2]PHE(4-CH2NH2) NEISSERIA MENINGITIDIS ZN-DEPENDENT APN (S)-2-[4-(AMINOMETHYL)BENZYL]-3-[(R)-1-AMPHENYLPROPYL(HYDROXY)PHOSPHORYL]PROPANOIC ACID HYDROLASE-HINHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED, SINGLE-POINT MODIFICATIONS IN THE PHOSPHINIC DIPEPTIDE STRUCTURE YIELD HIGHLY POTENT SELECTIVE INHIBITORS OF NEUTRAL AMINOPEPTIDASES. J.MED.CHEM. V. 57 8140 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:905;
A:904;
A:906;
A:907;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:911;
A:915;
A:910;
A:916;
A:917;
A:918;
A:912;
A:914;
A:913;
A:909;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
ZN A:908;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
IMD A:903;
Invalid;
none;
submit data
69.085 C3 H5 N2 c1c[n...
32Q A:901;
Valid;
none;
Ki = 9 nM
390.413 C20 H27 N2 O4 P c1ccc...
32R A:902;
Valid;
none;
Ki = 9 nM
390.413 C20 H27 N2 O4 P c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4QHP 1.6 Å EC: 3.4.11.2 CRYSTAL STRUCTURE OF AMINOPEPTIDASE N IN COMPLEX WITH THE PH DIPEPTIDE ANALOGUE LL-(R,S)-HPHEP[CH2]PHE(4-CH2NH2) NEISSERIA MENINGITIDIS ZN-DEPENDENT APN (S)-2-[4-(AMINOMETHYL)BENZYL]-3-[(R)-1-AMPHENYLPROPYL(HYDROXY)PHOSPHORYL]PROPANOIC ACID HYDROLASE-HINHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED, SINGLE-POINT MODIFICATIONS IN THE PHOSPHINIC DIPEPTIDE STRUCTURE YIELD HIGHLY POTENT SELECTIVE INHIBITORS OF NEUTRAL AMINOPEPTIDASES. J.MED.CHEM. V. 57 8140 2014
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4QHP Ki = 9 nM 32Q C20 H27 N2 O4 P c1ccc(cc1)....
2 4QIR Ki = 112 nM 379 C18 H23 N2 O4 P c1ccc(cc1)....
3 4QUO Ki = 12 nM 3DZ C20 H27 N2 O4 P c1ccc(cc1)....
4 4QPE - 37E C8 H19 N2 O3 P C1CCC(CC1)....
5 4QME Ki = 302 nM 37B C19 H24 N O4 P c1ccc(cc1)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4QHP Ki = 9 nM 32Q C20 H27 N2 O4 P c1ccc(cc1)....
2 4QIR Ki = 112 nM 379 C18 H23 N2 O4 P c1ccc(cc1)....
3 4QUO Ki = 12 nM 3DZ C20 H27 N2 O4 P c1ccc(cc1)....
4 4QPE - 37E C8 H19 N2 O3 P C1CCC(CC1)....
5 4QME Ki = 302 nM 37B C19 H24 N O4 P c1ccc(cc1)....
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: 32Q; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 32R 1 1
2 32Q 1 1
3 37B 0.810345 0.909091
4 BEY 0.810345 0.909091
5 3DZ 0.705882 1
6 379 0.605634 0.854167
Ligand no: 2; Ligand: 32R; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 32R 1 1
2 32Q 1 1
3 37B 0.810345 0.909091
4 BEY 0.810345 0.909091
5 3DZ 0.705882 1
6 379 0.605634 0.854167
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4QHP; Ligand: 32Q; Similar sites found with APoc: 113
This union binding pocket(no: 1) in the query (biounit: 4qhp.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5CX6 CDP 0.992908
2 2YIV YIV 1.06707
3 4DV8 0LX 1.3308
4 4XNV BUR 1.42518
5 3DWB RDF 1.49254
6 4Q86 AMP 1.53584
7 3ZPG 5GP 1.57068
8 1Y79 GLY ASP 1.61765
9 1Y79 LYS TRP 1.61765
10 1Q1Y BB2 2.09424
11 2YB9 HA0 2.15517
12 5A3Y VAL LYS 2.37226
13 3HBV ALA LYS ALA SER GLN ALA ALA 2.38095
14 5MZI FYK 2.38612
15 2GCG DGY 2.41379
16 1FBL HTA 2.43243
17 2W14 WR2 2.47525
18 1YKD CMP 2.51256
19 5M37 9SZ 2.6087
20 5M36 9SZ 2.62009
21 5KD8 TNR 2.68336
22 4CA5 3EF 2.71647
23 5O7E 9NB 2.79898
24 6CS8 F9Y 2.9703
25 5KDX GAL TNR 2.98851
26 3AHO 3A2 3.01418
27 3B9Z CO2 3.09278
28 4MGA 27L 3.13725
29 3TL1 JRO 3.14465
30 5AAV GW5 3.1746
31 4TV1 36M 3.18725
32 2OKL BB2 3.24324
33 1R55 097 3.27103
34 1ZED PNP 3.30579
35 4DD8 BAT 3.36538
36 4BXK 1IU 3.49762
37 5AMC GLY NIY 3.49762
38 4MRP GSH 3.58306
39 3M6P BB2 3.62694
40 1Q3A NGH 3.63636
41 3OZV ECN 3.72208
42 4WZV E40 3.75
43 4WKI 3PW 3.82979
44 3ZQE DXC 3.93443
45 5L44 K26 3.95315
46 1R6N 434 4.2654
47 1ZVX FIN 4.29448
48 3G5K BB2 4.37158
49 1WS1 BB2 4.48718
50 4JE7 BB2 4.56853
51 2FV5 541 4.5977
52 4B52 RDF 4.60526
53 1BKC INN 4.6875
54 5EY0 GTP 4.74453
55 4TMN 0PK 4.74684
56 1NF8 BOG 4.83092
57 3CH6 NAP 4.8951
58 3CH6 311 4.8951
59 1ATL 0QI 4.9505
60 4AIG FLX 4.97512
61 1HFS L04 5
62 3Q2H QHF 5.05051
63 3UWB BB2 5.19481
64 3WV1 WHH 5.26316
65 1MMQ RRS 5.29412
66 2IOY RIP 5.30035
67 5V4R MGT 5.55556
68 3C88 ARG ARG GLY CYS NH2 5.55556
69 2GBB CIT 5.76923
70 1OYF MHN 5.78512
71 1RM8 BAT 5.91716
72 4I90 CHT 5.94059
73 3E3U NVC 6.09137
74 1NU4 MLA 6.18557
75 5LX9 OLB 6.18893
76 3EYY MLI 6.2069
77 4AR8 IP8 GLY PRO ALA 6.34518
78 2TCL RO4 6.50888
79 4V3I ASP LEU THR ARG PRO 6.61479
80 2J83 BAT 6.87023
81 4K90 MLA 6.94087
82 4DR9 BB2 7.29167
83 5MTE BB2 7.29927
84 1LQY BB2 7.6087
85 1YP1 LYS ASN LEU 7.92079
86 6H8S FSZ 8.30565
87 6BTN E8M 8.91089
88 2OYH GLY HIS ARG PRO 9.09091
89 4DW4 U5P 10.1796
90 1G27 BB1 10.7143
91 2VWA PTY 10.8911
92 3ZVS MLI 11.25
93 1KUK PCA LYS TRP 11.33
94 3N7S 3N7 11.4583
95 1RL4 BRR 11.7021
96 3O01 DXC 12.013
97 3KP6 SAL 13.245
98 5UGW GSH 13.7143
99 5W7B MYR 14.455
100 2NV2 GLN 14.7059
101 5LWY OLB 14.9533
102 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 15.5172
103 4KX8 L2O VAL VAL ASP 17.5676
104 4OGQ 7PH 18.9189
105 4IN9 SER TRP PHE PRO 19.2771
106 5Z84 CHD 19.7279
107 5ZCO CHD 19.7279
108 5W97 CHD 19.7279
109 2Y69 CHD 20
110 1S17 GNR 20
111 2VJ8 HA2 24.5499
112 2XQ0 BES 27.3734
113 4GAA BES 28.4072
Pocket No.: 2; Query (leader) PDB : 4QHP; Ligand: 32R; Similar sites found with APoc: 12
This union binding pocket(no: 2) in the query (biounit: 4qhp.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 3O84 HTJ 2.02206
2 2ITM XUL 2.06612
3 1V9N NDP 2.22222
4 6FHO FAD 2.25564
5 1MVN PCO 3.34928
6 4ITH RCM 3.40136
7 1UPR 4IP 4.87805
8 5H86 BCO 5.35714
9 1NU4 MLA 6.18557
10 5L0S UDP 7.14286
11 1QSR ACO 7.40741
12 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 8.42105
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