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 1256 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 1068 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 922 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 0LK 0.609195 0.836364
4 0LJ 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: 98
This union binding pocket(no: 1) in the query (biounit: 4i54.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3TY3 GGG 0.01549 0.42889 1.13314
2 4BCN T9N 0.01097 0.41723 1.33333
3 3BP1 GUN 0.01837 0.40334 1.37931
4 3ODU ITD 0.04053 0.4036 1.41643
5 4YVN EBS 0.02863 0.41291 1.69972
6 3HQP FDP 0.02728 0.40139 1.80361
7 1SS4 GSH 0.0026 0.47325 1.96078
8 3A16 PXO 0.005783 0.46793 1.983
9 2PNC CLU 0.03178 0.40922 1.983
10 2J5B TYE 0.005532 0.4555 2.01149
11 1SQL GUN 0.004555 0.46014 2.05479
12 3I0O ADP 0.01731 0.41504 2.0649
13 5KJW 53C 0.04066 0.40263 2.26629
14 3FHR P4O 0.00843 0.41211 2.38095
15 1UPR 4IP 0.03478 0.40505 2.43902
16 2QHS OCA 0.002483 0.45772 2.53165
17 2IF8 ADP 0.002366 0.46943 2.54958
18 5M8T 0TR 0.01784 0.42405 2.54958
19 1WAP TRP 0.02291 0.40171 2.66667
20 4AU8 Z3R 0.02173 0.41002 2.7027
21 5L2R MLA 0.02407 0.41217 2.83286
22 2QHV OC9 0.003426 0.45561 2.85714
23 5BW4 SAM 0.01717 0.40115 2.99625
24 3FW3 GLC 0.03265 0.41089 3.00752
25 2D24 XYS XYS 0.01295 0.43164 3.11615
26 2B9J ADP 0.01663 0.40504 3.11615
27 4CR6 MAN 0.02888 0.40749 3.32103
28 1NBU PH2 0.0199 0.40821 3.36134
29 2GQS C2R 0.002186 0.45104 3.37553
30 3GD9 GLC BGC BGC BGC 0.01889 0.40934 3.68272
31 2VF7 ADP 0.0248 0.40345 3.68272
32 5AVF TAU 0.02485 0.41091 3.89105
33 4OKD GLC GLC GLC 0.01332 0.43053 3.96601
34 3VSV XYS 0.01425 0.42846 3.96601
35 3DOO SKM 0.02911 0.40757 3.97112
36 1K0E TRP 0.02772 0.40104 3.97351
37 2VN9 GVD 0.02153 0.41417 3.98671
38 3TW1 AHN 0.04605 0.40251 4.21941
39 5E9G GLV 0.03244 0.41011 4.24929
40 1IGW PYR 0.03444 0.40922 4.24929
41 1GXS BEZ 0.03912 0.40618 4.44444
42 5EWK P34 0.01413 0.42937 4.5
43 3X01 AMP 0.01724 0.42443 4.53258
44 4WOE ADP 0.02118 0.41997 4.53258
45 2Z49 AMG 0.01141 0.43598 4.62963
46 2Z48 A2G 0.01151 0.42754 4.62963
47 2W5P CL8 0.02364 0.41778 4.69799
48 2VZ6 FEF 0.02595 0.40247 4.79233
49 4UP4 GAL NAG 0.02175 0.41463 4.81586
50 4UCI ADN 0.03736 0.40316 4.81586
51 4UP4 NDG 0.03629 0.40121 4.81586
52 4UP4 NAG 0.03629 0.40121 4.81586
53 5XVQ 8GC 0.02339 0.41602 4.92958
54 1WW5 SGA BGC 0.04889 0.40072 5
55 3L8H FX1 0.007045 0.42384 5.02793
56 2V7O DRN 0.02311 0.41255 5.05952
57 3JU6 ANP 0.03891 0.40456 5.09915
58 1R6N 434 0.007602 0.44319 5.21327
59 1OPB RET 0.009723 0.4093 5.22388
60 4A91 GLU 0.02069 0.4123 5.36913
61 2YKL NLD 0.007228 0.43001 5.55556
62 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 0.03635 0.4074 5.66572
63 5TH5 MET 0.03791 0.40627 5.70342
64 3SJK LYS PRO VAL LEU ARG THR ALA 0.02124 0.42298 5.78947
65 5VAD PRO 0.01337 0.41307 5.94901
66 5E8J SAH 0.02444 0.40034 6.08974
67 3GUZ PAF 0.04276 0.40128 6.25
68 1W2D ADP 0.005061 0.4421 6.79245
69 5F90 GLA GAL BGC 5VQ 0.04519 0.40687 7.05128
70 4FE2 AIR 0.009001 0.42945 7.05882
71 4RI1 ACO 0.001878 0.43782 7.52688
72 4BTV RB3 0.009523 0.43982 7.55814
73 2AF6 BRU 0.03324 0.40911 7.75194
74 4B4Q A2G GAL NAG FUC GAL GLC 0.01155 0.43283 7.94702
75 3JQ3 ADP 0.03044 0.40254 8.2153
76 5CLO NS8 0.006494 0.44692 8.47458
77 4GDX GLU 0.02024 0.41932 8.49858
78 5F7Y GLC GAL NAG GAL FUC A2G 0.02252 0.40554 8.49858
79 1JJE BYS 0.01078 0.40415 8.55856
80 2TPI ILE VAL 0.01666 0.40176 8.62069
81 3ZJX BOG 0.02034 0.41909 8.65052
82 4JGP PYR 0.004108 0.46006 8.75576
83 1FHX 4IP 0.02341 0.41644 9.30233
84 1FAO 4IP 0.01786 0.42273 9.52381
85 5LDQ NAP 0.02813 0.40072 10.1695
86 1TZD ADP 0.001107 0.48718 10.1818
87 4YSX MLI 0.01383 0.43011 10.2564
88 5TVF CGQ 0.01473 0.41471 10.5882
89 5NCF 8T5 0.04135 0.40313 10.6195
90 1F8I GLV 0.01983 0.41715 10.7649
91 1GT4 UNA 0.01669 0.40497 11.3208
92 1I7M CG 0.02472 0.41103 11.9403
93 4WNP 3RJ 0.01138 0.41645 12.5436
94 1PVC ILE SER GLU VAL 0.01591 0.43983 13.2353
95 3SAO DBH 0.004119 0.44931 16.25
96 3ALT MLB 0.02403 0.41793 16.5605
97 1ZEI CRS 0.0413 0.40316 16.9811
98 3H9R TAK 0.01906 0.41693 17.4312
Pocket No.: 2; Query (leader) PDB : 4I54; Ligand: 1C1; Similar sites found: 36
This union binding pocket(no: 2) in the query (biounit: 4i54.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5F7J ADE 0.04311 0.40278 1.5625
2 5XQL C2E 0.01199 0.43889 1.71821
3 5AHO TLA 0.04188 0.40126 1.78571
4 3SIX GDP 0.01894 0.40928 1.81818
5 5TV6 PML 0.02831 0.40795 2.08333
6 2JKY 5GP 0.01096 0.41725 2.34742
7 4TS1 TYR 0.04271 0.40237 2.50784
8 5GVR LMR 0.04489 0.40422 2.99145
9 3ALN ANP 0.002897 0.45434 3.0581
10 1I1Q TRP 0.03068 0.40612 3.125
11 4JLS 3ZE 0.02553 0.41677 3.94737
12 4HNN LYS 0.03481 0.40848 4.04624
13 1U26 IHS 0.02691 0.40168 4.1543
14 2BVE PH5 0.02041 0.42395 4.20168
15 3LN9 FLC 0.002038 0.49249 4.24929
16 4Y8D 49J 0.02152 0.41839 4.41176
17 1TIQ COA 0.01726 0.40769 4.44444
18 4DYG MES 0.03949 0.4049 4.5082
19 5CDH TLA 0.003947 0.43032 4.7619
20 1HGX 5GP 0.01145 0.42845 4.91803
21 1JS8 MAN MAN BMA 0.03546 0.41121 5.09915
22 1U0J ADP 0.01785 0.41841 5.24345
23 1NX0 ALA LYS ALA ILE ALA 0.03894 0.41184 5.78035
24 1YQC GLV 0.0192 0.40552 5.88235
25 4F8L AES 0.01927 0.41611 6.2069
26 1DZK PRZ 0.01202 0.41173 7.00637
27 1Z4O GL1 0.01572 0.40965 7.23982
28 2D6M LBT 0.02007 0.41283 7.54717
29 2AL2 2PG 0.01891 0.40932 7.93201
30 3CM2 X23 0.03704 0.41124 8.46154
31 2WGH DTP 0.02858 0.40037 9.06516
32 3CQL NAG 0.03234 0.40595 9.87654
33 4YEE 4CQ 0.04352 0.40193 15.5556
34 1FWV SGA MAG FUC 0.04267 0.4064 16.4179
35 1Z0N BCD 0.006031 0.45757 16.6667
36 1S9D AFB 0.02454 0.40732 18.9024
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