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 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)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 (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: 32Q; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 32R 1 1
2 32Q 1 1
3 BEY 0.810345 0.909091
4 37B 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 BEY 0.810345 0.909091
4 37B 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: 64
This union binding pocket(no: 1) in the query (biounit: 4qhp.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4DV8 0LX 0.0002659 0.4769 1.3308
2 4XNV BUR 0.009563 0.42821 1.42518
3 3ZPG 5GP 0.02995 0.41263 1.57068
4 1Y79 LYS TRP 0.00009263 0.42127 1.61765
5 1Q1Y BB2 0.005433 0.41981 2.09424
6 2YB9 HA0 0.02879 0.4078 2.15517
7 5A3Y VAL LYS 0.006312 0.4372 2.37226
8 3HBV ALA LYS ALA SER GLN ALA ALA 0.002709 0.43837 2.38095
9 2GCG DGY 0.01721 0.41632 2.41379
10 2W14 WR2 0.002388 0.43642 2.47525
11 1YKD CMP 0.007064 0.40707 2.51256
12 4ARF IP8 GLY PRO ALA 0.00006872 0.50205 2.79188
13 5KDX GAL TNR 0.004005 0.45062 2.98851
14 3AHO 3A2 0.0006974 0.4448 3.01418
15 3B9Z CO2 0.04121 0.40226 3.09278
16 4MGA 27L 0.007265 0.43952 3.13725
17 3TL1 JRO 0.02903 0.40052 3.14465
18 2OKL BB2 0.005907 0.41053 3.24324
19 1R55 097 0.00788 0.42499 3.27103
20 5AMC GLY NIY 0.007127 0.42718 3.49762
21 4MRP GSH 0.04687 0.40521 3.58306
22 3M6P BB2 0.002181 0.40379 3.62694
23 1Q3A NGH 0.001491 0.46117 3.63636
24 4WZV E40 0.00221 0.42355 3.75
25 4WKI 3PW 0.002423 0.44068 3.82979
26 5L44 K26 0.001048 0.41026 3.95315
27 3G5K BB2 0.001723 0.43855 4.37158
28 1WS1 BB2 0.0007306 0.45546 4.48718
29 4B52 RDF 0.001074 0.40613 4.60526
30 3DBK RDF 0.001842 0.42903 4.65116
31 1BKC INN 0.001603 0.44921 4.6875
32 4TMN 0PK 0.002473 0.40455 4.74684
33 1NF8 BOG 0.0238 0.40897 4.83092
34 3CH6 NAP 0.02297 0.4113 4.8951
35 1ATL 0QI 0.001678 0.42513 4.9505
36 4AIG FLX 0.00143 0.45667 4.97512
37 3Q2H QHF 0.005914 0.40699 5.05051
38 3WV1 WHH 0.01025 0.41401 5.26316
39 1MMQ RRS 0.001124 0.44255 5.29412
40 5V4R MGT 0.002232 0.45845 5.55556
41 1OYF MHN 0.01202 0.42631 5.78512
42 1RM8 BAT 0.003413 0.44849 5.91716
43 3E3U NVC 0.0006707 0.46204 6.09137
44 3EYY MLI 0.01832 0.41435 6.2069
45 4AR8 IP8 GLY PRO ALA 0.000009047 0.542 6.34518
46 2TCL RO4 0.002908 0.41678 6.50888
47 4V3I ASP LEU THR ARG PRO 0.01393 0.42191 6.61479
48 4K90 MLA 0.002722 0.47749 6.94087
49 4DR9 BB2 0.0007087 0.45606 7.29167
50 1LQY BB2 0.001695 0.43463 7.6087
51 1YP1 LYS ASN LEU 0.002517 0.45527 7.92079
52 2OYH GLY HIS ARG PRO 0.009203 0.41306 9.09091
53 1G27 BB1 0.0007344 0.44639 10.7143
54 2VWA PTY 0.01586 0.40795 10.8911
55 3ZVS MLI 0.002841 0.42788 11.25
56 3N7S 3N7 0.01243 0.42688 11.4583
57 1RL4 BRR 0.01272 0.41907 11.7021
58 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 0.0000003376 0.48029 15.5172
59 4KX8 L2O VAL VAL ASP 0.0000000174 0.62096 17.5676
60 4IN9 SER TRP PHE PRO 0.002757 0.45427 19.2771
61 1S17 GNR 0.00251 0.42319 20
62 2VJ8 HA2 0.0000003147 0.44723 24.5499
63 2XQ0 BES 0.0000002275 0.50645 27.3734
64 4GAA BES 0.00000005914 0.64113 28.4072
Pocket No.: 2; Query (leader) PDB : 4QHP; Ligand: 32R; Similar sites found: 7
This union binding pocket(no: 2) in the query (biounit: 4qhp.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ITM XUL 0.01674 0.40979 2.06612
2 1V9N NDP 0.02771 0.41701 2.22222
3 1UPR 4IP 0.01598 0.41866 4.87805
4 5H86 BCO 0.03058 0.41061 5.35714
5 1NU4 MLA 0.001979 0.42294 6.18557
6 5L0S UDP 0.007829 0.43029 7.14286
7 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 0.03494 0.40969 8.42105
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