Structure of PDB 9gd3 Chain W Binding Site BS03

Receptor Information

>9gd3 Chain W (length=864) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

PTRFSNRQNKTVNYNIDYSDDDLLDFHGIDIVINHRLKDLNNCKENYEFL
IKWTDESHLHNTWETYESIGQVRGLKRLDNYCKQFIIEDQQVRLDPYVTA
EDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDGTSQLQYLVKWRRL
NYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRFEKL
SVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAF
ISWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRD
TIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDE
AHRLKNAESSLYESLNSFKVANRMLITGTPLQNNIKELAALVNFLMPGRF
TIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTERIL
RVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYL
FDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRV
LIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSND
FVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHV
MVYRLVSKDTVEEEVLERARKKMILEYAIIDMDSIGESEVRALYKAILKF
GNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKVLF
NFKGVKSLNAESLLSRVEDLKYLKNLINSNYKDDPLKFSLGNNTPKPVQN
WSSNWTKEEDEKLLIGVFKYGYGSWTQIRDDPFLGITDKIFLKKVPGAIH
LGRRVDYLLSFLRG

Ligand information

Ligand ID

ADP

InChI

InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1

InChIKey

XTWYTFMLZFPYCI-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N

Formula

C10 H15 N5 O10 P2

Name

ADENOSINE-5'-DIPHOSPHATE

PDB chain

9gd3 Chain W Residue 1501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	9gd3 Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT.
Resolution	3.0 Å
Binding residue (original residue number in PDB)	Q380 G404 L405 G406 K407 T408 V409 W447 N779 R807 I808
Binding residue (residue number reindexed from 1)	Q216 G240 L241 G242 K243 T244 V245 W283 N615 R643 I644
Annotation score	4

External links

PDB	RCSB:9gd3, PDBe:9gd3, PDBj:9gd3
PDBsum	9gd3
PubMed	39270644
UniProt	P32657\|CHD1_YEAST Chromo domain-containing protein 1 (Gene Name=CHD1)

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