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Receptor
PDB id Resolution Class Description Source Keywords
4I54 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 H375S COR COMPLEX WITH DMJ-II-121 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 HIV GP120 ENTRY INHIBITOR STRUCTURE-BASED DRUG DESIGN THERMODYNAMICS VIRAL INHIBITION DMJ-II-121 CD4-MIMETIC PROTEIN-INHIBITOR COMPLEX CLADE A/E CD4 EXTRACELLULAR
Ref.: STRUCTURE-BASED DESIGN AND SYNTHESIS OF AN HIV-1 EN INHIBITOR EXPLOITING X-RAY AND THERMODYNAMIC CHARACTERIZATION. ACS MED CHEM LETT V. 4 338 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG A:503;
B:507;
B:508;
A:509;
B:502;
B:506;
B:505;
B:503;
A:508;
A:510;
B:504;
A:504;
A:507;
A:506;
A:505;
Invalid;
Invalid;
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;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
1C1 A:501;
B:501;
Valid;
Valid;
none;
none;
Kd = 110 nM
404.846 C19 H20 Cl F N5 O2 c1ccc...
EPE A:502;
B:510;
Invalid;
Invalid;
none;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4I54 2.5 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 H375S COR COMPLEX WITH DMJ-II-121 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 HIV GP120 ENTRY INHIBITOR STRUCTURE-BASED DRUG DESIGN THERMODYNAMICS VIRAL INHIBITION DMJ-II-121 CD4-MIMETIC PROTEIN-INHIBITOR COMPLEX CLADE A/E CD4 EXTRACELLULAR
Ref.: STRUCTURE-BASED DESIGN AND SYNTHESIS OF AN HIV-1 EN INHIBITOR EXPLOITING X-RAY AND THERMODYNAMIC CHARACTERIZATION. ACS MED CHEM LETT V. 4 338 2013
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4DKQ Kd = 0.25 uM 0LK C18 H17 Cl F N5 O2 [H]/N=C(N)....
2 4DVX - 0M5 C16 H19 Cl F N3 O2 c1cc(c(cc1....
3 4I54 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
4 4DVW - 0M4 C16 H19 Cl F N3 O2 c1cc(c(cc1....
5 4DKP Kd = 1.9 uM 0LL C17 H15 Cl F N3 O2 c1ccc2c(c1....
6 4RZ8 ic50 ~ 270 nM 3ZM C22 H25 Cl N4 O2 S Cc1c(sc(n1....
7 5U6E - 82M C18 H18 Cl F N4 O2 S Cc1c(sc(n1....
8 4DVT - 0LZ C18 H17 Cl F N3 O2 c1ccc2c(c1....
9 4DKR Kd = 0.3 uM 0LJ C18 H17 Cl F N5 O2 [H]/N=C(/N....
10 4DVV - 0M1 C15 H19 Cl F N3 O4 CC1(O[C@H]....
11 4DKO Kd = 0.3 uM 0LM C18 H25 Cl F N3 O2 CC1(CC(CC(....
12 4DVS - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4DKQ Kd = 0.25 uM 0LK C18 H17 Cl F N5 O2 [H]/N=C(N)....
2 4DVX - 0M5 C16 H19 Cl F N3 O2 c1cc(c(cc1....
3 4I54 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
4 4DVW - 0M4 C16 H19 Cl F N3 O2 c1cc(c(cc1....
5 4DKP Kd = 1.9 uM 0LL C17 H15 Cl F N3 O2 c1ccc2c(c1....
6 4RZ8 ic50 ~ 270 nM 3ZM C22 H25 Cl N4 O2 S Cc1c(sc(n1....
7 5U6E - 82M C18 H18 Cl F N4 O2 S Cc1c(sc(n1....
8 4DVT - 0LZ C18 H17 Cl F N3 O2 c1ccc2c(c1....
9 4DKR Kd = 0.3 uM 0LJ C18 H17 Cl F N5 O2 [H]/N=C(/N....
10 4DVV - 0M1 C15 H19 Cl F N3 O4 CC1(O[C@H]....
11 4DKO Kd = 0.3 uM 0LM C18 H25 Cl F N3 O2 CC1(CC(CC(....
12 4DVS - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
13 4I53 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 4DKQ Kd = 0.25 uM 0LK C18 H17 Cl F N5 O2 [H]/N=C(N)....
2 4DVX - 0M5 C16 H19 Cl F N3 O2 c1cc(c(cc1....
3 4I54 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
4 4DVW - 0M4 C16 H19 Cl F N3 O2 c1cc(c(cc1....
5 4DKP Kd = 1.9 uM 0LL C17 H15 Cl F N3 O2 c1ccc2c(c1....
6 4RZ8 ic50 ~ 270 nM 3ZM C22 H25 Cl N4 O2 S Cc1c(sc(n1....
7 5U6E - 82M C18 H18 Cl F N4 O2 S Cc1c(sc(n1....
8 4DVT - 0LZ C18 H17 Cl F N3 O2 c1ccc2c(c1....
9 4DKR Kd = 0.3 uM 0LJ C18 H17 Cl F N5 O2 [H]/N=C(/N....
10 4DVV - 0M1 C15 H19 Cl F N3 O4 CC1(O[C@H]....
11 4DKO Kd = 0.3 uM 0LM C18 H25 Cl F N3 O2 CC1(CC(CC(....
12 4DVS - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
13 4I53 Kd = 110 nM 1C1 C19 H20 Cl F N5 O2 c1ccc2c(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 1C1; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 1C1 1 1
2 0LL 0.641975 0.727273
3 0LJ 0.609195 0.836364
4 0LK 0.609195 0.836364
5 0LZ 0.483871 0.655738
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4I54; Ligand: 1C1; Similar sites found with APoc: 119
This union binding pocket(no: 1) in the query (biounit: 4i54.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 3ZZL TRP None
2 3TY3 GGG 1.13314
3 3BP1 GUN 1.37931
4 3VCA PRO 1.69972
5 3HQP FDP 1.80361
6 3A16 PXO 1.983
7 4RF7 ARG 1.983
8 1KJ8 GAR 1.983
9 4GN8 ASO 2.00669
10 3LKF PC 2.00669
11 2J5B TYE 2.01149
12 1SQL GUN 2.05479
13 6G33 5ID 2.0649
14 4MOB ADP 2.10843
15 5OCG 9R5 2.1164
16 5KJW 53C 2.26629
17 6FA4 D1W 2.31214
18 2QHS OCA 2.53165
19 6FOF LAT 2.55102
20 5GG9 8GM 2.63158
21 1WAP TRP 2.66667
22 5Z5I XYP 2.83286
23 5L2R MLA 2.83286
24 5M90 JIF 2.83286
25 4OYA 1VE 2.83286
26 2QHV OC9 2.85714
27 3FW3 GLC 3.00752
28 3ZZQ TRP 3.07692
29 3EWK FAD 3.0837
30 5LY1 PPI 3.11615
31 2D24 XYS XYS 3.11615
32 2WPB ZZI 3.28947
33 1NBU PH2 3.36134
34 2GQS C2R 3.37553
35 4NFE BEN 3.37553
36 1RYD GLC 3.39943
37 5XIO HFG 3.39943
38 2F2U M77 3.39943
39 1ZGS XMM 3.39943
40 1F5F DHT 3.41463
41 4ZU3 4SD 3.52423
42 5H9Y BGC BGC BGC BGC 3.68272
43 3GD9 GLC BGC BGC BGC 3.68272
44 2Z3U CRR 3.68272
45 2WDQ CBE 3.7415
46 1LES GLC FRU 3.84615
47 4OKD GLC GLC GLC 3.96601
48 2UXR ICT 3.96601
49 4YJK URA 3.96825
50 3DOO SKM 3.97112
51 1K0E TRP 3.97351
52 2VN9 GVD 3.98671
53 2BVE PH5 4.20168
54 1IGW PYR 4.24929
55 1TIQ COA 4.44444
56 1GXS BEZ 4.44444
57 1VAY AZA 4.52962
58 2P7Q GG6 4.53258
59 4WOE ADP 4.53258
60 1FUR MLT 4.53258
61 5XLS URA 4.53258
62 2Z49 AMG 4.62963
63 2Z48 A2G 4.62963
64 1SDW IYT 4.77707
65 2VZ6 FEF 4.79233
66 4UP4 GAL NAG 4.81586
67 4UP4 NAG 4.81586
68 4UP4 NDG 4.81586
69 5YW5 ADE 5.02793
70 3L8H FX1 5.02793
71 2V7O DRN 5.05952
72 5NLM IOS 5.09915
73 3JU6 ANP 5.09915
74 1O9U ADZ 5.14286
75 6DZN AE3 5.16432
76 1R6N 434 5.21327
77 4A91 GLU 5.36913
78 3FSY SCA 5.42169
79 4IN9 SER TRP PHE PRO 5.42169
80 2YKL NLD 5.55556
81 5TH5 MET 5.70342
82 5VAD PRO 5.94901
83 5E9W SAH 6.08974
84 1MFI FHC 6.14035
85 6FOG OXL 6.25
86 2TOH HBI 6.41399
87 3CBC DBS 6.56566
88 5YSI NCA 6.57895
89 4PTN PYR 6.70554
90 5F90 GLA GAL BGC 5VQ 7.05128
91 5F90 GLA GAL 7.05128
92 2BMB PMM 7.08215
93 4RI1 ACO 7.52688
94 4BTV RB3 7.55814
95 5HWV MBN 7.69231
96 3ZZS TRP 7.69231
97 2AF6 BRU 7.75194
98 4B4Q A2G GAL NAG FUC GAL GLC 7.94702
99 5CLO NS8 8.47458
100 4GDX GLU 8.49858
101 5F7Y GLC GAL NAG GAL FUC A2G 8.49858
102 1JPA ANP 8.49858
103 2WEL K88 8.66667
104 4JGP PYR 8.75576
105 2XOC ADP 8.81226
106 1M26 GAL A2G 9.02256
107 2X1L MET 9.06516
108 5LDQ NAP 10.1695
109 1TZD ADP 10.1818
110 4YSX MLI 10.2564
111 6C4A PYR 10.7649
112 1F9V ADP 11.0482
113 6D5H FV7 11.3314
114 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 13.1579
115 3SAO DBH 16.25
116 3ALT MLB 16.5605
117 1ZEI CRS 16.9811
118 3H9R TAK 17.4312
119 6D61 4AA 21.5385
Pocket No.: 2; Query (leader) PDB : 4I54; Ligand: 1C1; Similar sites found with APoc: 45
This union binding pocket(no: 2) in the query (biounit: 4i54.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 1HBK COA None
2 3M2W L8I 1.33779
3 6AMI TRP 1.41643
4 5F7J ADE 1.5625
5 4YVN EBS 1.69972
6 2PNC CLU 1.983
7 5OKT 9XK 1.983
8 1P19 IMP 2.26244
9 2JKY 5GP 2.34742
10 1IS3 LAT 2.54958
11 2HIM ASP 2.54958
12 3ACC 5GP 2.76243
13 1YFS ALA 2.83286
14 5NFB 8VT 2.84091
15 5GVR LMR 2.99145
16 3ALN ANP 3.0581
17 2JBH 5GP 3.11111
18 1I1Q TRP 3.125
19 1XX6 ADP 3.14136
20 5TCI MLI 3.26087
21 1U1J MET 3.68272
22 2BQP GLC 3.84615
23 4JLS 3ZE 3.94737
24 1KDK DHT 3.9548
25 3VSV XYS 3.96601
26 1QB7 ADE 4.23729
27 3LN9 FLC 4.24929
28 3X01 AMP 4.53258
29 3SRV S19 4.69314
30 5CDH TLA 4.7619
31 1HGX 5GP 4.91803
32 1WW5 SGA BGC 5
33 4C01 QY9 5.09915
34 1U0J ADP 5.24345
35 4QYN RTL 5.26316
36 3KV8 FAH 5.7554
37 2JIG PD2 5.80357
38 1DCP HBI 6.73077
39 1QAW TRP 6.75676
40 1W2D ADP 6.79245
41 2D6M LBT 7.54717
42 3ZJX BOG 8.65052
43 1LK7 DER 9.60699
44 1TD2 PXL 9.7561
45 1Z0N BCD 16.6667
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