Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T52297 Target Info
Target Name Oxysterols receptor LXR-alpha (NR1H3)
Synonyms Nuclear receptor subfamily 1 group H member 3; Nuclear receptor LXRalpha; Nuclear orphan receptor LXR-alpha; Liver X receptor alpha; LXRalpha; LXRA
Target Type Patented-recorded Target
Gene Name NR1H3
Biochemical Class Nuclear hormone receptor
UniProt ID
NR1H3_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: GW-3965 Ligand Info
Structure Description X-ray structure of GW3965 synthetic agonist bound to the LXR-alpha PDB:3IPQ
Method X-ray diffraction Resolution 2.00 Å Mutation No [1]
PDB Sequence
QLSPEQLGMI
214
EKLVAAQQTP
237
WPEARQQRFA
255
HFTELAIVSV
265
QEIVDFAKQL
275

PGFLQLSRED
285
QIALLKTSAI
295
EVMLLETSRR
305
YNPGSESITF
315
LKDFSYNRED
325

FAKAGLQVEF
335
INPIFEFSRA
345
MNELQLNDAE
355
FALLIAISIF
365
SADRPNVQDQ
375

LQVERLQHTY
385
VEALHAYVSI
395
HHPHDRLMFP
405
RMLMKLVSLR
415
TLSSVHSEQV
425

FALRLQDKKL
435
PPLLSEIWDV
445
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3IPQ
Interaction of chain A with chain BInteraction of chain B with chain AInteraction of chain A with chain 965Interaction of chain 965 with chain AInteraction of chain A with chain SO4Interaction of chain SO4 with chain AInteraction of chain B with chain SO4Interaction of chain SO4 with chain BChain 965: [3-(3-{[2-chloro-3-(trifluoromethyl)benzyl](2,2-diphenylethyl)amino}propoxy)phenyl]acetic acid9..Chain SO4: SULFATE IONS..Chain 9652: [3-(3-{[2-chloro-3-(trifluoromethyl)benzyl](2,2-diphenylethyl)amino}propoxy)phenyl]acetic acid9..Chain SO42: SULFATE IONS..Chain A: Oxysterols receptor LXR-alphaAChain B: Nuclear receptor coactivator 1B
Nodes:
OProtein
▢Nucleotide
◇Chemical
▢Biopolymer

Lines:
Interactions at 4 Å

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Note: VAST+ finds other macromolecular structures that have a similar biological unit. To do this, VAST+ takes into consideration the complete set of 3D domains that VAST identified within a query structure, throughout all of its component protein molecules, and finds other macromolecular structures that have a similar set of proteins/3D domains.

PDB ID:
Note: VAST identifies 3D domains (substructures) within each protein structure in the Molecular Modeling Database (MMDB), and then finds other protein structures that have one or more similar 3D domains, using purely geometric criteria. You have two ways to do a VAST search.

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2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below.

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Chain ID List:
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The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"):
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Residue Color File:
The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube".

Custom File:

1.
Score to Color: 0: 50: 100:
or

2.
You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.
refnum,11,12,,21,22,,10C,11C,20C
1TUP_A,100,101,,,132,,,,
1TUP_B,110,111,,141,142,,,,
1TUP_C,,,,,,,200,201,230
The first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure.

To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.

Custom File:

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Chain IDs:



(Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".)

All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

Chain IDs:

The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain:



(Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".)

All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

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Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.


Option 1:

Option 2:
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

Chain IDs:

Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.


Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".
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2fofc contour at default threshold or at: σ




fofc contour at default threshold or at: σ





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fofc contour at default threshold or at: σ
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Potential contour at: kT/e(25.6mV at 298K)

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Surface with max potential at: kT/e(25.6mV at 298K)

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Cube File:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.

Potential contour at: kT/e(25.6mV at 298K)

Grid Size: Salt Concentration: M

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Surface with max potential at: kT/e(25.6mV at 298K)

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Cube URL in the same host:


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Symmetry:       

Distance: Contact Type:


1. Choose interaction types and their thresholds:
Hydrogen Bonds    
Å   
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5. and select new sets
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2.

1. Select sets below or use your current selection.


2.

1. Select sets below or use your current selection:


2. Overall maximum RMSD: Å

3.

1. Select sets below:

2.

1. Select sets below:

2.

1. Select sets below:

2.

1. Select sets below:

2.

  Hold Ctrl key to select multiple nodes/lines.
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    Scale:

Hold Ctrl key to select multiple nodes.   
        Scale:

Hold Ctrl key to select multiple nodes.   
        Scale:

051015202530
Expected position error (Angstroms)

Contour at: σ
Contour at: σ
Contour at: % of maximum EM values
1. Select the first set:

2. Sphere with a radius: Å

3. Select the second set to apply the sphere:

4. the sphere around the first set of atoms

interacting/contacting residue pairs in a file
Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

1. Extracellular membrane Z-axis position: Å

2. intracellular membrane Z-axis position: Å

3. the adjusted membranes

Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

1. Z-axis position of the first X-Y plane: Å

2. Z-axis position of the second X-Y plane: Å

3. the region between the planes to Defined Sets

1. Text:
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4. Pick TWO atoms while holding "Alt" key
5.
1. Text:
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3. Color:
4.
Color for all labels:

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3.
1. Pick TWO atoms while holding "Alt" key
2. Color:
3.
1. Select two sets
First set:
Second set:
2. Color:

3.
1. Select two sets
First set:
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3. Line radius:

4. Color:

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6.    
1. Select a set:

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5. Opacity:

6.    
1. Select sets for pairwise distances
First sets:
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2.
Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated.

1. Select sets for pairwise angles
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Second sets:
2.
1. Pick TWO atoms while holding "Alt" key
2.
Line Radius:    (for stabilizers, hydrogen bonds, distance lines, default 0.1)
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Cross-Linkage Radius:    (for cross-linkages, default 0.4)
Trace Radius:    (for C alpha trace, O3' trace, default 0.4)
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Protein Ribbon Width:    (for helix and sheet ribbons, default 1.3)
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Back Light:    (for the light strength of the back light, default 0.2)

3. Thickness:
Line Radius:    (for stabilizers, hydrogen bonds, distance lines, default 0.1)
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Cross-Linkage Radius:    (for cross-linkages, default 0.4)
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Ribbon Thickness:    (for helix and sheet ribbons, nucleotide ribbons, default 0.2)
Protein Ribbon Width:    (for helix and sheet ribbons, default 1.3)
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4. Show Glycan Cartoon:    (0: hide, 1: show, default 0)

5. Show Membrane:    (0: hide, 1: show, default 1)

6. Enlarge Command Window:    (0: Regular, 1: Large, default 0)

   
Note: The following parameters will be saved in cache. You just need to set them once.





Note: Show exons for all isoforms of the protein in the same gene as specified below.

NCBI Gene ID:    

Position of the first residue in Sequences & Annotations window:

Name:



1. URLs Used in Browsers

Please copy one of the URLs below. They show the same result.
(To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.)

Original URL with commands:


Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub)


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2. Commands Used in Jupyter Noteboook

Please copy the following commands into a cell in Jupyter Notebook to show the same result.
More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook.



Annotations: 
All  Conserved Domains  ClinVar  Functional Sites  
Custom  3D Domains  SNPs  PTM (UniProt)  
Disulfide Bonds  Interactions  Cross-Linkages  Transmembrane  
Ig Domains  



Zoom: mouse wheel;     Move: left button;     Select Multiple Nodes: Ctrl Key and drag an Area   
       
Force on Nodes:
   Label Size:    
Internal Edges:
Solvent Accessible Surface Area(SASA) calculated using the EDTSurf algorithm:
(0-20% out is considered "in". 50-100% out is considered "out".)

Toal: Å2

Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively.

Middle Percentage(White): %



Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100.

Min Percentage: %
Max Percentage: %


Select residue based on B-factor/pLDDT. The values are in the range of 0-100.

Min B-factor/pLDDT: %
Max B-factor/pLDDT: %


X: Y: Z:
Vector 1, X: Y: Z:
Vector 2, X: Y: Z:



The angle is: degree.

0: 4: 8: 12:
1: 5: 9: 13:
2: 6: 10: 14:
3: 7: 11: 15:
Choose an Ig template for selected residues:



Choose an Ig template to align with selected residues:



Residue
Distance (Å)
PHE254
4.197
PHE257
3.554
THR258
3.873
LEU260
3.396
ALA261
3.613
VAL263
4.494
SER264
3.573
GLU267
3.762
ILE295
3.747
MET298
3.559
LEU299
3.623
GLU301
4.050
THR302
3.151
ARG305
2.857
ILE313
3.754
THR314
4.348
Residue
Distance (Å)
PHE315
3.359
LEU316
2.872
PHE326
3.661
LEU331
3.871
PHE335
3.582
ILE336
3.727
ILE339
3.409
PHE340
3.733
HIS421
3.652
GLN424
3.677
VAL425
3.823
LEU428
3.651
LEU435
3.279
LEU439
4.943
TRP443
3.472
Ligand Name: L-783483 Ligand Info
Structure Description X-ray structure of benzisoxazole synthetic agonist bound to the LXR-alpha PDB:3IPS
Method X-ray diffraction Resolution 2.26 Å Mutation No [1]
PDB Sequence
QLSPEQLGMI
214
EKLVAAQQVT
236
PWPSREARQQ
252
RFAHFTELAI
262
VSVQEIVDFA
272

KQLPGFLQLS
282
REDQIALLKT
292
SAIEVMLLET
302
SRRYNPGSES
312
ITFLKDFSYN
322

REDFAKAGLQ
332
VEFINPIFEF
342
SRAMNELQLN
352
DAEFALLIAI
362
SIFSADRPNV
372

QDQLQVERLQ
382
HTYVEALHAY
392
VSIHHPHDRL
402
MFPRMLMKLV
412
SLRTLSSVHS
422

EQVFALRLQD
432
KKLPPLLSEI
442
WDVH
Loading data...
Dynamically generated for selected residues.
Nodes can be dragged or clicked.
    
Label:

Selection: Name:   

Defined Sets:
Set Operations:

Select:
Name:
   
Specification Tips:

Note: VAST+ finds other macromolecular structures that have a similar biological unit. To do this, VAST+ takes into consideration the complete set of 3D domains that VAST identified within a query structure, throughout all of its component protein molecules, and finds other macromolecular structures that have a similar set of proteins/3D domains.

PDB ID:
Note: VAST identifies 3D domains (substructures) within each protein structure in the Molecular Modeling Database (MMDB), and then finds other protein structures that have one or more similar 3D domains, using purely geometric criteria. You have two ways to do a VAST search.

Option 1, search with your selection (all residues are selected by default) in the loaded structures:
Searching against: Medium-redundancy Subset of PDB ? All of PDB

Option 2, search with PDB ID and chain name:
PDB ID:   Chain Name:


Option 3, search with a PDB file:
PDB File:
Searching against: Medium-redundancy Subset of PDB ? All of PDB

1. your selection (all residues are selected by default) in the loaded structures to Foldseek web server.

2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below.

The PDB chain IDs are the same as the record names such as "1HHO_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v4" is "P69905".

Chain ID List:
BCIF/MMTF ID:
PDB ID:
Note: AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100:
  Very high (pLDDT > 90)
  Confident (90 > pLDDT > 70)
  Low (70 > pLDDT > 50)
  Very low (pLDDT < 50)

AlphaFold Uniprot ID:



PAE Map:
NCBI Protein Accession:
Orientations of Proteins in Membranes(OPM) PDB ID:
Note: Several PDB files could be concatenated into a single PDB file. Use the line "ENDMDL" to separate PDB files.

PDB File:
Multiple PDB Files:
The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"):
{"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...}

Residue Color File:
The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube".

Custom File:

1.
Score to Color: 0: 50: 100:
or

2.
You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.
refnum,11,12,,21,22,,10C,11C,20C
1TUP_A,100,101,,,132,,,,
1TUP_B,110,111,,141,142,,,,
1TUP_C,,,,,,,200,201,230
The first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure.

To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.

Custom File:

Enter the PDB IDs or MMDB IDs of the structures:

ID1:       ID2:

VAST+ based on VAST:    

VAST+ based on TM-align:

Enter two AlphaFold Uniprot IDs:

ID1:       ID2:

All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

Chain IDs:



(Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".)

All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

Chain IDs:

The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain:



(Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".)

All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

Chain IDs:

Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.


Option 1:

Option 2:
All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).

Chain IDs:

Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50.


Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".
If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page".

Mutations:


ID Type: PDB IDAlphaFold UniProt ID

Show Mutation in: Current PageNew Page



Mol2 File:
SDF File:
XYZ File:
AlphaFold PAE File:

File type:
URL in the same host:
Multiple mmCIF Files:
mmCIF ID:
MMDB or PDB ID:




Note: The "biological unit" is the biochemically active form of a biomolecule,
List of PDB, MMDB, or AlphaFold UniProt structures:



or


Note: The "biological unit" is the biochemically active form of a biomolecule,
Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the BLAST search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used.

Protein Sequence ID(NCBI protein accession of a sequence):
or FASTA sequence:


Aligned Protein Accession (or a chain of a PDB):
The sequence to structure prediction is done via ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here.

FASTA sequence:


Your note will be saved in the HTML file when you click "File > Save File > iCn3D PNG Image".


Protein/Gene name:
PubChem CID/Name/InchI:
Chemical SMILES:
Multiple iCn3D PNG images:
State file:
Since January 6, 2021, you can show the original view with the archived version of iCn3D by pasting your URL below and click "Show Originial View". Note the version in the parameter "v" was used to replace "full.html" with "full_[v].html" in the URL.

Share Link URL:


Selection file:
Collection File:

You can load a collection of structures via a file. Here are some example files

Collection file:


Structures:





Preference file:
Note: Always load a PDB file before loading map files. If you don't specify the threshold below, a default one will be chosen.


2fofc contour at default threshold or at: σ




fofc contour at default threshold or at: σ





Note: Always load a PDB file before loading map files. If you don't specify the threshold below, a default one will be chosen.


2fofc contour at default threshold or at: σ
URL in the same host:



fofc contour at default threshold or at: σ
URL in the same host:




Click in the input box to use the color picker:

Custom Color:
Grid Size: Salt Concentration: M

Potential contour at: kT/e(25.6mV at 298K)



Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation.

Grid Size: Salt Concentration: M

Surface with max potential at: kT/e(25.6mV at 298K)

Surface: Opacity: Wireframe:



Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation.

Potential contour at: kT/e(25.6mV at 298K)

Grid Size: Salt Concentration: M

PQR File:

Phi File:

Cube File:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.

Surface with max potential at: kT/e(25.6mV at 298K)

Surface: Opacity: Wireframe:

Grid Size: Salt Concentration: M

PQR File:

Phi File:

Cube File:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.

Potential contour at: kT/e(25.6mV at 298K)

Grid Size: Salt Concentration: M

PQR URL in the same host:

Phi URL in the same host:

Cube URL in the same host:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.

Surface with max potential at: kT/e(25.6mV at 298K)

Surface: Opacity: Wireframe:

Grid Size: Salt Concentration: M

PQR URL in the same host:

Phi URL in the same host:

Cube URL in the same host:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.


Symmetry:       

Distance: Contact Type:


1. Choose interaction types and their thresholds:
Hydrogen Bonds    
Å   
Salt Bridge/Ionic    
Å   
Contacts/Interactions    
Å   
Halogen Bonds    
Å   
π-Cation    
Å   
π-Stacking    
Å   
2. Select the first set:
3. Select the second set:
4.

Sort Interactions on:

to show two lines of residue nodes

to show map

with atom details

to show interactions with strength parameters in 0-200:
Helix or Sheet: Coil or Nucleotide: Disulfide Bonds:
Hydrogen Bonds: Salt Bridge/Ionic: Contacts:
Halogen Bonds: π-Cation: π-Stacking:
(Note: you can also adjust thresholds at #1 to add/remove interactions.)


5. and select new sets
1. Select sets below
or use your current selection:


2.

1. Select sets below or use your current selection.


2.

1. Select sets below or use your current selection:


2. Overall maximum RMSD: Å

3.

1. Select sets below:

2.

1. Select sets below:

2.

1. Select sets below:

2.

1. Select sets below:

2.

  Hold Ctrl key to select multiple nodes/lines.
Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts
Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking

        Scale:

Hold Ctrl key to select multiple nodes.   
        Scale:

Note: Nodes/Residues can be dragged. Both nodes and dashed lines/interactions can be clicked to select residues.    
Color legend for interactions (dashed lines):
Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts
Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking

    Scale:

Hold Ctrl key to select multiple nodes.   
        Scale:

Hold Ctrl key to select multiple nodes.   
        Scale:

051015202530
Expected position error (Angstroms)

Contour at: σ
Contour at: σ
Contour at: % of maximum EM values
1. Select the first set:

2. Sphere with a radius: Å

3. Select the second set to apply the sphere:

4. the sphere around the first set of atoms

interacting/contacting residue pairs in a file
Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

1. Extracellular membrane Z-axis position: Å

2. intracellular membrane Z-axis position: Å

3. the adjusted membranes

Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

1. Z-axis position of the first X-Y plane: Å

2. Z-axis position of the second X-Y plane: Å

3. the region between the planes to Defined Sets

1. Text:
2. Size:
3. Color:
4. Pick TWO atoms while holding "Alt" key
5.
1. Text:
2. Size:
3. Color:
4.
Color for all labels:

1. Pick TWO atoms while holding "Alt" key
2. Line Color:
3.
1. Pick TWO atoms while holding "Alt" key
2. Color:
3.
1. Select two sets
First set:
Second set:
2. Color:

3.
1. Select two sets
First set:
Second set:
2. Line style:

3. Line radius:

4. Color:

5. Opacity:

6.    
1. Select a set:

2. Shape:

3. Radius:

4. Color:

5. Opacity:

6.    
1. Select sets for pairwise distances
First sets:
Second sets:
2.
Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated.

1. Select sets for pairwise angles
First sets:
Second sets:
2.
1. Pick TWO atoms while holding "Alt" key
2.
Line Radius:    (for stabilizers, hydrogen bonds, distance lines, default 0.1)
Coil Radius:    (for coils, default 0.3)
Stick Radius:    (for sticks, default 0.4)
Cross-Linkage Radius:    (for cross-linkages, default 0.4)
Trace Radius:    (for C alpha trace, O3' trace, default 0.4)
Ribbon Thickness:    (for helix and sheet ribbons, nucleotide ribbons, default 0.2)
Protein Ribbon Width:    (for helix and sheet ribbons, default 1.3)
Nucleotide Ribbon Width:    (for nucleotide ribbons, default 0.8)
Ball Scale:    (for styles 'Ball and Stick' and 'Dot', default 0.3)
   
Note: The following parameters will be saved in cache. You just need to set them once.

1. Shininess:    (for the shininess of the 3D objects, default 40)

2. Three directional lights:
Key Light:    (for the light strength of the key light, default 0.8)
Fill Light:    (for the light strength of the fill light, default 0.4)
Back Light:    (for the light strength of the back light, default 0.2)

3. Thickness:
Line Radius:    (for stabilizers, hydrogen bonds, distance lines, default 0.1)
Coil Radius:    (for coils, default 0.3)
Stick Radius:    (for sticks, default 0.4)
Cross-Linkage Radius:    (for cross-linkages, default 0.4)
Trace Radius:    (for C alpha trace, O3' trace, default 0.4)
Ribbon Thickness:    (for helix and sheet ribbons, nucleotide ribbons, default 0.2)
Protein Ribbon Width:    (for helix and sheet ribbons, default 1.3)
Nucleotide Ribbon Width:    (for nucleotide ribbons, default 0.8)
Ball Scale:    (for styles 'Ball and Stick' and 'Dot', default 0.3)

4. Show Glycan Cartoon:    (0: hide, 1: show, default 0)

5. Show Membrane:    (0: hide, 1: show, default 1)

6. Enlarge Command Window:    (0: Regular, 1: Large, default 0)

   
Note: The following parameters will be saved in cache. You just need to set them once.





Note: Show exons for all isoforms of the protein in the same gene as specified below.

NCBI Gene ID:    

Position of the first residue in Sequences & Annotations window:

Name:



1. URLs Used in Browsers

Please copy one of the URLs below. They show the same result.
(To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.)

Original URL with commands:


Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub)


Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".)


2. Commands Used in Jupyter Noteboook

Please copy the following commands into a cell in Jupyter Notebook to show the same result.
More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook.



Annotations: 
All  Conserved Domains  ClinVar  Functional Sites  
Custom  3D Domains  SNPs  PTM (UniProt)  
Disulfide Bonds  Interactions  Cross-Linkages  Transmembrane  
Ig Domains  



Zoom: mouse wheel;     Move: left button;     Select Multiple Nodes: Ctrl Key and drag an Area   
       
Force on Nodes:
   Label Size:    
Internal Edges:
Solvent Accessible Surface Area(SASA) calculated using the EDTSurf algorithm:
(0-20% out is considered "in". 50-100% out is considered "out".)

Toal: Å2

Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively.

Middle Percentage(White): %



Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100.

Min Percentage: %
Max Percentage: %


Select residue based on B-factor/pLDDT. The values are in the range of 0-100.

Min B-factor/pLDDT: %
Max B-factor/pLDDT: %


X: Y: Z:
Vector 1, X: Y: Z:
Vector 2, X: Y: Z:



The angle is: degree.

0: 4: 8: 12:
1: 5: 9: 13:
2: 6: 10: 14:
3: 7: 11: 15:
Choose an Ig template for selected residues:



Choose an Ig template to align with selected residues:



Residue
Distance (Å)
PHE254
4.177
PHE257
3.307
THR258
3.810
LEU260
2.958
ALA261
3.861
VAL263
4.808
SER264
3.776
GLU267
4.245
ILE295
4.142
MET298
3.345
LEU299
3.986
GLU301
3.320
THR302
3.320
ARG305
2.829
Residue
Distance (Å)
PHE315
3.377
LEU316
3.810
PHE326
4.493
LEU331
4.220
PHE335
3.123
ILE339
4.411
HIS421
3.438
GLN424
3.592
VAL425
4.025
LEU428
3.417
LEU435
3.478
LEU439
4.752
TRP443
2.925
Ligand Name: T0901317 Ligand Info
Structure Description Crystal structure of the LXRalfa-RXRbeta LBD heterodimer PDB:1UHL
Method X-ray diffraction Resolution 2.90 Å Mutation No [2]
PDB Sequence
MSPEQLGMIE
215
KLVAAQQQCN
225
RRSFEARQQR
253
FAHFTELAIV
263
SVQEIVDFAK
273

QLPGFLQLSR
283
EDQIALLKTS
293
AIEVMLLETS
303
RRYNPGSESI
313
TDFSYNREDF
326

AKAGLQVEFI
336
NPIFEFSRAM
346
NELQLNDAEF
356
ALLIAISIFS
366
ADRPNVQDQL
376

QVERLQHTYV
386
EALHAYVSIH
396
HPHDRLMFPR
406
MLMKLVSLRT
416
LSSVHSEQVF
426

ALRLQDKKLP
436
PLLSEIWDV
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .444 or .4442 or .4443 or :3444;style chemicals stick;color identity;select .B:254 or .B:257 or .B:258 or .B:260 or .B:261 or .B:264 or .B:295 or .B:298 or .B:299 or .B:302 or .B:305 or .B:326 or .B:331 or .B:335 or .B:339 or .B:421 or .B:424 or .B:425 or .B:428 or .B:439 or .B:443; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE254
4.070
PHE257
3.795
THR258
4.120
LEU260
3.924
ALA261
3.374
SER264
2.837
ILE295
4.339
MET298
2.882
LEU299
3.528
THR302
2.431
ARG305
4.956
Residue
Distance (Å)
PHE326
3.858
LEU331
3.266
PHE335
4.279
ILE339
2.983
HIS421
2.433
GLN424
3.543
VAL425
4.673
LEU428
4.872
LEU439
3.511
TRP443
3.737
Ligand Name: 2-Chloro-4-{1'-[(2r)-2-Hydroxy-3-Methyl-2-(Trifluoromethyl)butanoyl]-4,4'-Bipiperidin-1-Yl}-N,N-Dimethylbenzamide Ligand Info
Structure Description Identification of LXRbeta selective agonists for the treatment of Alzheimer's Disease PDB:5HJS
Method X-ray diffraction Resolution 1.72 Å Mutation No [3]
PDB Sequence
QLSPEQLGMI
50
EKLVAAQQLR
70
VTPWPSREAR
86
QQRFAHFTEL
96
AIVSVQEIVD
106

FAKQLPGFLQ
116
LSREDQIALL
126
KTSAIEVMLL
136
ETSRRYNPGS
146
ESITFLKDFS
156

YNREDFAKAG
166
LQVEFINPIF
176
EFSRAMNELQ
186
LNDAEFALLI
196
AISIFSADRP
206

NVQDQLQVER
216
LQHTYVEALH
226
AYVSIHHPHD
236
RLMFPRMLMK
246
LVSLRTLSSV
256

HSEQVFALRL
266
QDKKLPPLLS
276
EIWDVH
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .668 or .6682 or .6683 or :3668;style chemicals stick;color identity;select .A:90 or .A:93 or .A:94 or .A:96 or .A:97 or .A:99 or .A:100 or .A:103 or .A:131 or .A:134 or .A:135 or .A:137 or .A:138 or .A:141 or .A:150 or .A:151 or .A:152 or .A:165 or .A:166 or .A:167 or .A:171 or .A:257 or .A:260 or .A:261 or .A:264 or .A:271 or .A:275 or .A:279; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE90
3.788
PHE93
3.650
THR94
3.487
LEU96
3.374
ALA97
3.659
VAL99
4.047
SER100
3.872
GLU103
3.435
ILE131
3.757
MET134
3.579
LEU135
4.921
GLU137
4.071
THR138
3.437
ARG141
2.890
Residue
Distance (Å)
THR150
4.873
PHE151
3.315
LEU152
3.103
ALA165
4.786
GLY166
4.943
LEU167
2.870
PHE171
3.681
HIS257
2.824
GLN260
3.091
VAL261
4.934
LEU264
3.391
LEU271
3.312
LEU275
3.949
TRP279
3.440
Ligand Name: 4-{[Methyl(3-{[7-propyl-3-(trifluoromethyl)-1,2-benzisoxazol-6-yl]oxy}propyl)carbamoyl]amino}benzoic acid Ligand Info
Structure Description X-ray structure of benzisoxazole urea synthetic agonist bound to the LXR-alpha PDB:3IPU
Method X-ray diffraction Resolution 2.40 Å Mutation No [1]
PDB Sequence
PQLSPEQLGM
213
IEKLVAAQQQ
223
CNRRSFSDRL
233
RVTPWPPHSR
247
EARQQRFAHF
257

TELAIVSVQE
267
IVDFAKQLPG
277
FLQLSREDQI
287
ALLKTSAIEV
297
MLLETSRRYN
307

PGSESITFLK
317
DFSYNREDFA
327
KAGLQVEFIN
337
PIFEFSRAMN
347
ELQLNDAEFA
357

LLIAISIFSA
367
DRPNVQDQLQ
377
VERLQHTYVE
387
ALHAYVSIHH
397
PHDRLMFPRM
407

LMKLVSLRTL
417
SSVHSEQVFA
427
LRLQDKKLPP
437
LLSEIWDV
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .O40 or .O402 or .O403 or :3O40;style chemicals stick;color identity;select .A:225 or .A:232 or .A:254 or .A:257 or .A:258 or .A:260 or .A:261 or .A:264 or .A:267 or .A:295 or .A:298 or .A:299 or .A:301 or .A:302 or .A:305 or .A:315 or .A:316 or .A:317 or .A:326 or .A:331 or .A:335 or .A:339 or .A:421 or .A:424 or .A:425 or .A:428 or .A:435 or .A:439 or .A:443; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN225
3.501
ARG232
3.044
PHE254
4.062
PHE257
3.313
THR258
3.782
LEU260
3.504
ALA261
3.608
SER264
3.870
GLU267
4.623
ILE295
3.794
MET298
3.780
LEU299
4.212
GLU301
4.005
THR302
3.809
ARG305
3.418
Residue
Distance (Å)
PHE315
3.206
LEU316
4.029
LYS317
4.687
PHE326
3.800
LEU331
3.705
PHE335
3.733
ILE339
4.324
HIS421
3.336
GLN424
4.073
VAL425
4.592
LEU428
3.248
LEU435
3.147
LEU439
3.945
TRP443
3.790
Ligand Name: Tert-Butyl 2-[[4-[ethanoyl(Methyl)amino]phenoxy]methyl]-5-(Trifluoromethyl)benzoate Ligand Info
Structure Description Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 4 PDB:5AVI
Method X-ray diffraction Resolution 2.70 Å Mutation No [4]
PDB Sequence
PQLSPEQLGM
213
IEKLVAAQQR
234
VTPWPPHSRE
248
ARQQRFAHFT
258
ELAIVSVQEI
268

VDFAKQLPGF
278
LQLSREDQIA
288
LLKTSAIEVM
298
LLETSRRYNP
308
GSESITFLKD
318

FSYNREDFAK
328
AGLQVEFINP
338
IFEFSRAMNE
348
LQLNDAEFAL
358
LIAISIFSAD
368

RPNVQDQLQV
378
ERLQHTYVEA
388
LHAYVSIHHP
398
HDRLMFPRML
408
MKLVSLRTLS
418

SVHSEQVFAL
428
RLQDKKLPPL
438
LSEIWDVH
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4KM or .4KM2 or .4KM3 or :34KM;style chemicals stick;color identity;select .A:254 or .A:257 or .A:258 or .A:260 or .A:261 or .A:264 or .A:295 or .A:298 or .A:299 or .A:301 or .A:302 or .A:305 or .A:315 or .A:326 or .A:331 or .A:335 or .A:339 or .A:421 or .A:424 or .A:425 or .A:428 or .A:435 or .A:439 or .A:443; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE254
4.120
PHE257
3.383
THR258
3.861
LEU260
3.525
ALA261
3.455
SER264
3.624
ILE295
3.399
MET298
3.701
LEU299
3.855
GLU301
3.724
THR302
3.599
ARG305
3.492
Residue
Distance (Å)
PHE315
3.566
PHE326
3.915
LEU331
3.458
PHE335
3.460
ILE339
3.797
HIS421
3.897
GLN424
3.380
VAL425
4.344
LEU428
3.379
LEU435
3.750
LEU439
4.887
TRP443
3.442
Ligand Name: 2-[4-[4-[[2-[(2-Methylpropan-2-Yl)oxycarbonyl]-3-Oxidanyl-4-(Trifluoromethyl)phenyl]methoxy]phenyl]phenyl]ethanoic Acid Ligand Info
Structure Description Crystal structure of LXRalpha in complex with tert-butyl benzoate analog, compound 32b PDB:5AVL
Method X-ray diffraction Resolution 2.80 Å Mutation No [4]
PDB Sequence
PQLSPEQLGM
213
IEKLVAAQQV
235
TPWREARQQR
253
FAHFTELAIV
263
SVQEIVDFAK
273

QLPGFLQLSR
283
EDQIALLKTS
293
AIEVMLLETS
303
RRYNPGSESI
313
TFLKDFSYNR
323

EDFAKAGLQV
333
EFINPIFEFS
343
RAMNELQLND
353
AEFALLIAIS
363
IFSADRPNVQ
373

DQLQVERLQH
383
TYVEALHAYV
393
SIHHPHDRLM
403
FPRMLMKLVS
413
LRTLSSVHSE
423

QVFALRLQDK
433
KLPPLLSEIW
443
DVHE
Click to Show 3D Structure of This Binding Site
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Residue
Distance (Å)
PHE254
3.655
PHE257
3.344
THR258
3.872
LEU260
3.579
ALA261
3.521
SER264
3.634
GLU267
4.366
ILE295
3.300
MET298
3.781
LEU299
3.680
GLU301
4.003
THR302
3.302
ARG305
2.930
THR314
4.205
Residue
Distance (Å)
PHE315
3.270
LEU316
2.731
PHE326
3.872
LEU331
3.335
PHE335
3.383
ILE339
3.580
HIS421
3.199
GLN424
3.286
VAL425
4.431
LEU428
3.259
LEU435
3.588
LEU439
4.866
TRP443
3.488
References  Top
REF 1 X-ray structures of the LXRalpha LBD in its homodimeric form and implications for heterodimer signaling. J Mol Biol. 2010 May 28;399(1):120-32.
REF 2 Crystal structure of the heterodimeric complex of LXRalpha and RXRbeta ligand-binding domains in a fully agonistic conformation. EMBO J. 2003 Sep 15;22(18):4625-33.
REF 3 Identification and in Vivo Evaluation of Liver X Receptor beta-Selective Agonists for the Potential Treatment of Alzheimer's Disease. J Med Chem. 2016 Apr 14;59(7):3489-98.
REF 4 Discovery and structure-guided optimization of tert-butyl 6-(phenoxymethyl)-3-(trifluoromethyl)benzoates as liver X receptor agonists. Bioorg Med Chem Lett. 2015 Sep 15;25(18):3914-20.

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