Structure of PDB 9gd2 Chain W Binding Site BS04

Receptor Information

>9gd2 Chain W (length=641) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GIDIVINHRLLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKRLD
NYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDS
QRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNREN
SKILPQYSSNYTSQRPRFEKLSVQPPFIKGGELRDFQLTGINWMAFLWSK
GDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPAWLDT
FEKWAPDLNCICYMGNQKSRDTIREYEFYTNPKTMKFNVLLTTYEYILKD
RAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQNN
IKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRL
KKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGFSLLNIMN
ELKKASNHPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQL
LTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRIS
IDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMA
RAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILEYAII

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

9gd2 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	9gd2 Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT.
Resolution	4.2 Å
Binding residue (original residue number in PDB)	E375 L376 R377 Q380 G404 G406 K407 T408 V409 W447 R807 I808
Binding residue (residue number reindexed from 1)	E182 L183 R184 Q187 G211 G213 K214 T215 V216 W254 R604 I605
Annotation score	4

External links

PDB	RCSB:9gd2, PDBe:9gd2, PDBj:9gd2
PDBsum	9gd2
PubMed	39270644
UniProt	P32657\|CHD1_YEAST Chromo domain-containing protein 1 (Gene Name=CHD1)

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