Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T34405 Target Info
Target Name Fractalkine (CX3CL1)
Synonyms Small-inducible cytokine D1; Small inducible cytokine D1; SCYD1; Neurotactin; NTT; FKN; CX3C membrane-anchored chemokine; C-X3-C motif chemokine 1; A-152E5.2
Target Type Literature-reported Target
Gene Name CX3CL1
UniProt ID
X3CL1_HUMAN
Ligand General Information  Top
Ligand Name Pyroglutamic Acid Ligand Info
Canonical SMILES C1CC(=O)NC1C(=O)O
InChI 1S/C5H7NO3/c7-4-2-1-3(6-4)5(8)9/h3H,1-2H2,(H,6,7)(H,8,9)/t3-/m0/s1
InChIKey ODHCTXKNWHHXJC-VKHMYHEASA-N
PubChem Compound ID 7405
Drug Binding Sites of Target  Top
PDB ID: 7XBX      Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with CX3CL1 and Gi1
Method Electron microscopy Resolution 3.40 Å Mutation Yes [1]
PDB Sequence
HHGVTKCNIT
11
CSKMTSKIPV
21
ALLIHYQQNQ
31
ASCCKRAIIL
41
ETRQHRLFCE
55

QWVKDAMQHL
65
DYIGDIVVFG
132
TVFLSIFYSV
142
IFAIGLVGNL
152
LVVFALTNSK
162

KPKSVTDIYL
172
LNLALSDLLF
182
VATLPFWTHY
192
LINEKGLHNA
202
MCKFTTAFFF
212

IGFFGSIFFL
222
TVISIDRYLA
232
IVLAANSMNN
242
RTVQHGVTIS
252
LGVWAAAILV
262

AAPQFMFTKQ
272
KENECCGDYP
282
EVLQEIWPVL
292
RNVETNFLGF
302
LLPLLIMSYC
312

YFRIIQTLFS
322
SKNHKKAKAI
332
KLILLVVIVF
342
FLFWTPYNVV
352
IFLETLKLYD
362

FFPSCDMRKD
372
LRLALSVTET
382
VAFSHCCLNP
392
LIYAFAGEKF
402
RRYLYHLY
Residue
Distance (Å)
HIS2
1.331
HIS3
3.356
VAL5
4.847
TRP189
4.211
THR208
2.190
PHE212
2.126
GLN266
3.265
Residue
Distance (Å)
PHE267
4.073
PHE269
4.497
THR270
2.791
CYS277
3.542
CYS278
4.250
GLY279
4.511
ARG293
2.241
PDB ID: 4XT1      Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1
Method X-ray diffraction Resolution 2.89 Å Mutation Yes [2]
PDB Sequence
HHGVTKCAIT
11
CSKMTSKIPV
21
ALLIHYQQNQ
31
ASCGKRAIIL
41
ETRQHRLFCA
51

DPKEQWVKDA
61
MQHLDRQ
Residue
Distance (Å)
HIS2
1.330
HIS3
4.507
Residue
Distance (Å)
VAL5
3.860
PDB ID: 7RKM      Structure of CX3CL1-US28-Gi-scFv16 in C-state
Method Electron microscopy Resolution 3.50 Å Mutation No [3]
PDB Sequence
HHGVTKCNIT
11
CSKMTSKIPV
21
ALLIHYQQNQ
31
ASCGKRAIIL
41
ETRQHRLFCA
51

DPKEQWVKDA
61
MQHLDRQ
Residue
Distance (Å)
HIS2
1.329
Residue
Distance (Å)
HIS3
3.899
PDB ID: 7RKF      Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state
Method Electron microscopy Resolution 4.00 Å Mutation No [3]
PDB Sequence
HHGVTKCNIT
11
CSKMTSKIPV
21
ALLIHYQQNQ
31
ASCGKRAIIL
41
ETRQHRLFCA
51

DPKEQWVKDA
61
MQHLDR
Click to Show 3D Structure of This Binding Site
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Residue
Distance (Å)
HIS2
1.329
HIS3
3.695
Residue
Distance (Å)
VAL5
3.708
References  Top
REF 1 Activation of the human chemokine receptor CX3CR1 regulated by cholesterol. Sci Adv. 2022 Jul;8(26):eabn8048.
REF 2 Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor. Science. 2015 Mar 6;347(6226):1113-7.
REF 3 Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins. doi:10.1126/sciadv.abl5442.

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