Receptor
PDB id Resolution Class Description Source Keywords
3W68 2.05 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF MOUSE ALPHA-TOCOPHEROL TRANSFER PROTEIN COMPLEX WITH ALPHA-TOCOPHEROL AND PHOSPHATIDYLINOSITOL-(4,5B ISPHOSPHATE MUS MUSCULUS ATAXIA VITAMIN E DEFICIENCY AVED TRANSFER PROTEIN TOCOPHVITAMIN E DISEASE MUTATION ALPHA-TOCOPHEROL TRANSFER ALPTOCOPHEROL PHOSPHATIDYL INOSITOL PHOSPHATES TRANSPORT PRO
Ref.: IMPAIRED ALPHA-TTP-PIPS INTERACTION UNDERLIES FAMIL VITAMIN E DEFICIENCY SCIENCE V. 340 1106 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
VIV C:301;
B:301;
D:301;
A:301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
430.706 C29 H50 O2 Cc1c(...
4PT A:302;
A:303;
B:303;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
716.35 C17 H36 O22 P4 CCC[C...
PBU B:302;
Valid;
none;
submit data
634.354 C17 H33 O19 P3 CCCC(...
PO4 D:302;
C:304;
C:302;
C:303;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3W68 2.05 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF MOUSE ALPHA-TOCOPHEROL TRANSFER PROTEIN COMPLEX WITH ALPHA-TOCOPHEROL AND PHOSPHATIDYLINOSITOL-(4,5B ISPHOSPHATE MUS MUSCULUS ATAXIA VITAMIN E DEFICIENCY AVED TRANSFER PROTEIN TOCOPHVITAMIN E DISEASE MUTATION ALPHA-TOCOPHEROL TRANSFER ALPTOCOPHEROL PHOSPHATIDYL INOSITOL PHOSPHATES TRANSPORT PRO
Ref.: IMPAIRED ALPHA-TTP-PIPS INTERACTION UNDERLIES FAMIL VITAMIN E DEFICIENCY SCIENCE V. 340 1106 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 3W68 - 4PT C17 H36 O22 P4 CCC[C@@H](....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 3W68 - 4PT C17 H36 O22 P4 CCC[C@@H](....
2 5MUG - VIV C29 H50 O2 Cc1c(c2c(c....
3 5MUE - VIV C29 H50 O2 Cc1c(c2c(c....
4 1OIP - VIV C29 H50 O2 Cc1c(c2c(c....
5 1R5L - VIV C29 H50 O2 Cc1c(c2c(c....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3W68 - 4PT C17 H36 O22 P4 CCC[C@@H](....
2 5MUG - VIV C29 H50 O2 Cc1c(c2c(c....
3 5MUE - VIV C29 H50 O2 Cc1c(c2c(c....
4 1OIP - VIV C29 H50 O2 Cc1c(c2c(c....
5 1R5L - VIV C29 H50 O2 Cc1c(c2c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VIV; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 VIT 1 1
2 VIV 1 1
Ligand no: 2; Ligand: 4PT; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 4PT 1 1
2 PBU 0.602564 0.9375
3 IP9 0.564706 0.9
4 5P5 0.5625 0.9375
5 PIB 0.5625 0.9375
6 PIZ 0.55814 0.9
7 DB4 0.551282 0.9375
8 3PI 0.536585 0.978723
9 52N 0.477778 0.882353
10 PIO 0.477778 0.882353
11 PIF 0.444444 0.882353
12 PII 0.406593 0.862745
Ligand no: 3; Ligand: PBU; Similar ligands found: 37
No: Ligand ECFP6 Tc MDL keys Tc
1 PBU 1 1
2 DB4 0.84127 1
3 PIB 0.818182 1
4 5P5 0.818182 1
5 52N 0.753425 0.938776
6 PIO 0.753425 0.938776
7 PIF 0.644737 0.938776
8 IP9 0.641026 0.918367
9 PIZ 0.632911 0.918367
10 4PT 0.602564 0.9375
11 PII 0.576923 0.918367
12 3PI 0.571429 0.957447
13 B7N 0.517241 0.9
14 T7X 0.478723 0.9
15 IBS 0.450704 0.787234
16 PSF 0.444444 0.684211
17 44E 0.432432 0.795918
18 P5S 0.423529 0.684211
19 PD7 0.421053 0.795918
20 CN3 0.420455 0.76
21 44G 0.419753 0.764706
22 CN6 0.413793 0.76
23 7PH 0.410256 0.795918
24 6PH 0.410256 0.795918
25 3PH 0.410256 0.795918
26 LPP 0.410256 0.795918
27 CD4 0.409639 0.76
28 7P9 0.405063 0.795918
29 PEF 0.404762 0.644068
30 PTY 0.404762 0.644068
31 PEH 0.404762 0.644068
32 PEV 0.404762 0.644068
33 8PE 0.404762 0.644068
34 PGT 0.4 0.764706
35 9PE 0.4 0.644068
36 LHG 0.4 0.764706
37 PEE 0.4 0.633333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3W68; Ligand: VIV; Similar sites found: 80
This union binding pocket(no: 1) in the query (biounit: 3w68.bio4) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F4S EFO 0.005428 0.43986 None
2 2IYG FMN 0.004382 0.43018 None
3 1EPB REA 0.005892 0.416 None
4 1YRX FMN 0.01119 0.40684 None
5 1UO5 PIH 0.004749 0.40277 None
6 4EVQ PHB 0.01974 0.40255 1.12782
7 3WYJ H78 0.01189 0.42274 1.18577
8 4B7P 9UN 0.009873 0.41457 1.30435
9 1C1L GAL BGC 0.01004 0.42466 1.45985
10 3OYW TDG 0.007707 0.43199 1.49254
11 1G27 BB1 0.00455 0.4137 1.78571
12 2WA4 069 0.003057 0.43766 1.8797
13 1H8S AIC 0.007601 0.42748 1.98413
14 2ZHL NAG GAL GAL NAG 0.01678 0.40219 2.02703
15 5C5T AKG 0.02627 0.40024 2.19298
16 2XK9 XK9 0.02161 0.4157 2.25564
17 1OGX EQU 0.004699 0.4245 2.29008
18 3RGA LSB 0.006493 0.41407 2.63158
19 3PUR 2HG 0.02966 0.40196 2.63158
20 5ML3 DL3 0.007296 0.41264 2.68456
21 3E2M E2M 0.002886 0.40228 2.7027
22 4L4J NAG NAG BMA MAN NAG 0.0006831 0.47597 2.71493
23 1OI6 TMP 0.03488 0.40331 2.92683
24 4XCP PLM 0.01159 0.42904 2.94118
25 4RFR RHN 0.002521 0.40198 2.95567
26 3CL5 SIO 0.004402 0.44499 3.00752
27 5HCN DAO 0.02674 0.40393 3.06513
28 2HFN FMN 0.007362 0.40797 3.26797
29 1ULE GLA GAL NAG 0.006308 0.43823 3.33333
30 4OPC FDA 0.03225 0.41608 3.38346
31 2ET1 GLV 0.0232 0.40922 3.48259
32 5DG2 GAL GLC 0.01258 0.40942 3.7037
33 3G58 988 0.01056 0.41594 3.7594
34 1FMB HYB 0.004764 0.42844 3.84615
35 5U9J GER 0.0313 0.40036 4.14201
36 1I7E IBS 0.02256 0.4087 4.15094
37 4DR9 BB2 0.01064 0.40424 4.16667
38 3V1S 0LH 0.02671 0.40006 4.88722
39 2AGC DAO 0.01229 0.41694 4.93827
40 2Z77 NCA 0.01702 0.41416 5.03597
41 2AXR ABL 0.02647 0.40513 5.26316
42 1N5S ADL 0.006694 0.41347 5.35714
43 1X0P FAD 0.0009335 0.40971 5.59441
44 3SAO DBH 0.01199 0.41556 5.625
45 3SAO NKN 0.02214 0.40008 5.625
46 3KDU NKS 0.004183 0.43311 5.6391
47 4R38 RBF 0.003351 0.41594 5.71429
48 2I74 MAN MAN MAN MAN 0.02976 0.40286 5.82011
49 4GCZ FMN 0.001694 0.4092 6.01504
50 1S17 GNR 0.002859 0.42253 6.11111
51 5T7I LAT NAG GAL 0.008661 0.4307 6.45161
52 1XMY ROL 0.005867 0.43314 6.76692
53 1XMU ROF 0.006798 0.41699 6.76692
54 1XM4 PIL 0.01319 0.40723 6.76692
55 4WVW SLT 0.001052 0.47168 6.94444
56 4OCT AKG 0.002127 0.45009 7.20721
57 4JH6 FCN 0.01341 0.41504 7.24638
58 4ZXA H8N 0.02068 0.40552 7.7381
59 5AIG VPR 0.01725 0.40543 8
60 2PR5 FMN 0.002945 0.42197 9.09091
61 3T50 FMN 0.004903 0.41228 9.375
62 1SGJ OAA 0.01988 0.40363 9.3985
63 4O4Z N2O 0.01691 0.40223 9.74026
64 1Q1Y BB2 0.01078 0.40761 9.94764
65 2Z6D FMN 0.007884 0.40324 10
66 1DZK PRZ 0.008182 0.40947 10.828
67 4EES FMN 0.005283 0.40746 11.3043
68 2QJY UQ2 0.02263 0.40808 12.406
69 2YOO K2B 0.002277 0.42686 14.2857
70 5L2J 70E 0.03697 0.40074 15.0376
71 3G08 FEE 0.008407 0.42344 15.1515
72 1LQY BB2 0.005559 0.41343 16.8478
73 1T0S BML 0.01338 0.40743 23.2558
74 2OKL BB2 0.007436 0.40778 25.4054
75 3RET SAL 0.01369 0.40273 35.6436
76 3RET PYR 0.01369 0.40273 35.6436
77 1AUA BOG 0.0002782 0.5064 41.3534
78 3HX3 RET 0.0008138 0.41486 41.7293
79 1O6U PLM 0.001255 0.44668 44.7368
80 1OLM VTQ 0.001016 0.41006 45.8647
Pocket No.: 2; Query (leader) PDB : 3W68; Ligand: 4PT; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3w68.bio2) has 3 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3W68; Ligand: 4PT; Similar sites found: 27
This union binding pocket(no: 3) in the query (biounit: 3w68.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BME GNP 0.01123 0.41827 None
2 4ZU3 4SD 0.01141 0.40282 1.76211
3 2PD4 DCN 0.03178 0.4188 1.8797
4 2PD4 NAD 0.03593 0.41441 1.8797
5 3CH6 311 0.03508 0.42959 2.63158
6 3CH6 NAP 0.03508 0.42959 2.63158
7 3RWO GDP 0.037 0.40369 3.24324
8 2XVE FAD 0.04668 0.41499 3.38346
9 3ETG GWD 0.02484 0.40436 3.38346
10 5T9F NAP 0.02316 0.42213 3.7594
11 5T9F TYR 0.03786 0.4101 3.7594
12 4B5P ACO 0.02906 0.40765 4
13 5A3T MMK 0.009968 0.43579 4.13534
14 2J8Z NAP 0.00988 0.42692 4.13534
15 4OR7 NAP 0.02045 0.41394 4.24242
16 154L NAG NAG NAG 0.02069 0.40023 4.86486
17 1ME8 RVP 0.02744 0.41003 5.26316
18 1DR1 NAP 0.02491 0.41733 5.29101
19 1DR1 HBI 0.02491 0.41733 5.29101
20 2W9S NDP 0.008602 0.43404 5.59006
21 2XVD AS6 0.02569 0.40751 5.6391
22 4MAF ADX 0.02985 0.40158 5.6391
23 1U26 IHS 0.01801 0.40057 6.76692
24 1N62 MCN 0.02702 0.41026 9.03614
25 5SXS AMP 0.01293 0.40133 10.9023
26 3HRD MCN 0.02643 0.4103 13.75
27 2XMY CDK 0.02059 0.44384 25.5639
Pocket No.: 4; Query (leader) PDB : 3W68; Ligand: VIV; Similar sites found: 14
This union binding pocket(no: 4) in the query (biounit: 3w68.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WKQ FMN 0.007542 0.40061 2.63158
2 4COQ SAN 0.01043 0.42264 3.64372
3 5AAV GW5 0.02561 0.40712 3.96825
4 3L5R 47X 0.02532 0.42113 5.26316
5 2Z8L NAG FUC SIA GAL 0.02325 0.40568 5.28846
6 3ET1 ET1 0.007108 0.40173 5.6391
7 4ZOM 4Q3 0.03834 0.40761 5.77778
8 5U98 1KX 0.02419 0.41034 6.06061
9 3WCA FPS 0.01012 0.40409 7.14286
10 2IDO TMP 0.02422 0.4053 7.52688
11 4X5S AZM 0.01331 0.41633 8.62069
12 4XBT FLC 0.004352 0.4146 10.9677
13 4XBT 3ZQ 0.005833 0.40897 10.9677
14 3N7S 3N7 0.02893 0.40139 16.6667
Pocket No.: 5; Query (leader) PDB : 3W68; Ligand: 4PT; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3w68.bio1) has 6 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3W68; Ligand: 4PT; Similar sites found: 11
This union binding pocket(no: 6) in the query (biounit: 3w68.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2D4V FLC 0.01388 0.41456 3.00752
2 4EIL NDP 0.02397 0.41044 3.7594
3 3ORQ ADP 0.0187 0.4092 3.7594
4 2X2M X2M 0.00484 0.43787 4.13534
5 3HKW IX6 0.003883 0.43532 4.51128
6 1XSE NDP 0.03211 0.41915 4.88722
7 3U4L ATP 0.02808 0.40909 4.88722
8 3MQG ACO 0.01885 0.41463 6.25
9 3RG9 NDP 0.04055 0.41327 9.16667
10 3RG9 WRA 0.04507 0.41327 9.16667
11 1W07 FAD 0.03983 0.40312 9.3985
Pocket No.: 7; Query (leader) PDB : 3W68; Ligand: 4PT; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 3w68.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3W68; Ligand: PBU; Similar sites found: 25
This union binding pocket(no: 8) in the query (biounit: 3w68.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JIF CU BLM 0.03891 0.40388 None
2 1WG8 SAM 0.01628 0.4192 2.25564
3 4V3C C 0.01478 0.41352 2.25564
4 1XDY MTE 0.02948 0.40048 2.63158
5 4RFR RHN 0.01569 0.41149 2.95567
6 2DC1 NAD 0.02836 0.41033 2.9661
7 2RH1 CAU 0.0223 0.40037 3.00752
8 2APC UDM 0.01987 0.40721 3.38346
9 4PNE SAH 0.03137 0.40232 3.97351
10 1XHL NDP 0.04887 0.40165 4.3771
11 4ZSI GLP 0.01405 0.40852 4.67836
12 4W6Z 8ID 0.03189 0.41567 5.26316
13 5CDH TLA 0.01666 0.41532 6.01504
14 3LGS ADE 0.01924 0.41085 6.01504
15 1WUR 8DG 0.0314 0.40288 6.36364
16 1N0U SO1 0.02557 0.40634 6.39098
17 2BNF UTP 0.005619 0.44308 7.46888
18 3ND6 ATP 0.027 0.41842 9.35672
19 4JGX PLM 0.002911 0.44266 10.8527
20 4UP3 FAD 0.04406 0.40869 12.406
21 4NAT 2W5 0.01695 0.43341 16.25
22 4NAT ADP 0.04546 0.43288 16.25
23 5ECP ATP 0.02631 0.42229 19.5489
24 5ECP JAA 0.02536 0.42229 19.5489
25 5ECP MET 0.02536 0.42229 19.5489
Pocket No.: 9; Query (leader) PDB : 3W68; Ligand: VIV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 3w68.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 3W68; Ligand: VIV; Similar sites found: 8
This union binding pocket(no: 10) in the query (biounit: 3w68.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5EW9 5VC 0.03918 0.41229 2.25564
2 3FUR Z12 0.0111 0.41228 2.63158
3 2WW2 SWA 0.02654 0.40257 3.00752
4 2Z6C FMN 0.005452 0.41026 4.65116
5 3P7N FMN 0.007098 0.40524 4.65116
6 4WUJ FMN 0.001953 0.40695 4.7619
7 2GJ5 VD3 0.01275 0.40202 6.17284
8 4YZC STU 0.01354 0.40087 7.5188
Pocket No.: 11; Query (leader) PDB : 3W68; Ligand: VIV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 3w68.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 3W68; Ligand: VIV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 3w68.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 3W68; Ligand: VIV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 3w68.bio5) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 3W68; Ligand: 4PT; Similar sites found: 16
This union binding pocket(no: 14) in the query (biounit: 3w68.bio3) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3NYQ AMP 0.0468 0.41677 2.25564
2 3NYQ MCA 0.0451 0.41677 2.25564
3 5LXM ADP 0.01999 0.40615 2.25564
4 4NG2 OHN 0.0268 0.40173 3.26087
5 4ZLU 4PW 0.02283 0.42266 3.38346
6 4ZLU ADP 0.02283 0.42266 3.38346
7 4C2W ANP 0.01376 0.40781 4.13534
8 1PHK ATP 0.01229 0.42517 4.51128
9 3CLH NAD 0.027 0.40813 5.26316
10 5CUQ NSC 0.04184 0.40136 5.26316
11 3IQE F42 0.04048 0.40049 5.26316
12 1XKD ICT 0.01826 0.4045 5.6391
13 1MDB AMP DBH 0.01476 0.40688 7.14286
14 3JVH HHV 0.04058 0.4001 11.4754
15 1V47 ADX 0.02717 0.4007 12.0301
16 3ANP DCC 0.04981 0.40081 17.6471
Pocket No.: 15; Query (leader) PDB : 3W68; Ligand: PBU; Similar sites found: 1
This union binding pocket(no: 15) in the query (biounit: 3w68.bio3) has 4 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3VRV YSD 0.0001689 0.50798 38.4615
Pocket No.: 16; Query (leader) PDB : 3W68; Ligand: VIV; Similar sites found: 9
This union binding pocket(no: 16) in the query (biounit: 3w68.bio3) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1L0I PSR 0.009559 0.43256 None
2 1GT6 OLA 0.01699 0.40032 2.63158
3 3GUZ PAF 0.02493 0.40358 2.84091
4 1KYZ FER 0.02581 0.40436 3.00752
5 3G5K BB2 0.01105 0.40184 6.01093
6 1WS1 BB2 0.009962 0.40389 7.69231
7 3KP6 SAL 0.01791 0.40368 8.60927
8 3KYQ DPV 0.02956 0.40011 13.5678
9 2Y69 CHD 0.01626 0.40922 24.2857
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