Structure of PDB 7rmp Chain D Binding Site BS05

Receptor Information
>7rmp Chain D (length=1032) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAKAISEQTGKELLYKFICTTSAIQNRFKYARVTPDTDWARLLQDHPWLL
SQNLVVKPDQLIKRRGKLGLVGVNLTLDGVKSWLKPRLGQEATVGKATGF
LKNFLIEPFVPHSQAEEFYVCIYATREGDYVLFHHEGGVDVGDVDAKAQK
LLVGVDEKLNPEDIKKHLLVHAPEDKKEILASFISGLFNFYEDLYFTYLE
INPLVVTKDGVYVLDLAAKVDATADYICKVKWGDIEFPPPFGREAYPEEA
YIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNEL
ANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVA
ATFKGIVRAIRDYQGPLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIP
IHVFGTETHMTAIVGMALGHRPIPGKSTTLFSRHTKAIVWGMQTRAVQGM
LDFDYVCSRDEPSVAAMVYPFTGDHKQKFYWGHKEILIPVFKNMADAMRK
HPEVDVLINFASLRSAYDSTMETMNYAQIRTIAIIAEGIPEALTRKLIKK
ADQKGVTIIGPATVGGIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVSR
SGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKM
IVVLGEIGGTEEYKICRGIKEGRLTKPIVCWCIGTCATMFSSEVQACANQ
ASETAVAKNQALKEAGVFVPRSFDELGEIIQSVYEDLVANGVIVPAQEVP
PPTVPMDYSWARELGLIRKPASFMTSICDERGQELIYAGMPITEVFKEEM
GIGGVLGLLWFQKRLPKYSCQFIEMCLMVTADHGPAVSGAHNTIICARAG
KDLVSSLTSGLLTIGDRFGGALDAAAKMFSKAFDSGIIPMEFVNKMKKEG
KLIMGIGHRVKSINNPDMRVQILKDYVRQHFPATPLLDYALEVEKITTSK
KPNLILNVAGLIGVAFVDMLRNCGSFTREEADEYIDIGALNGIFVLGRSM
GFIGHYLDQKRLKQGLYRHPWDDISYVLPEHM
Ligand information
Ligand IDQ5B
InChIInChI=1S/C27H42N7O22P3S/c1-26(2,20(40)23(41)30-4-3-14(35)29-5-6-60-16(38)8-27(44,25(42)43)7-15(36)37)10-53-59(50,51)56-58(48,49)52-9-13-19(55-57(45,46)47)18(39)24(54-13)34-12-33-17-21(28)31-11-32-22(17)34/h11-13,18-20,24,39-40,44H,3-10H2,1-2H3,(H,29,35)(H,30,41)(H,36,37)(H,42,43)(H,48,49)(H,50,51)(H2,28,31,32)(H2,45,46,47)/t13-,18-,19-,20+,24-,27+/m1/s1
InChIKeyIHVFHZGGMJDGGZ-VPXVXCNZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)C[C@@](CC(=O)O)(C(=O)O)O)O
CACTVS 3.385CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)C[C](O)(CC(O)=O)C(O)=O
CACTVS 3.385CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)C[C@@](O)(CC(O)=O)C(O)=O
OpenEye OEToolkits 2.0.7CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)CC(CC(=O)O)(C(=O)O)O)O
FormulaC27 H42 N7 O22 P3 S
Name(3S)-citryl-Coenzyme A;
(2~{S})-2-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-2-oxidanylidene-ethyl]-2-oxidanyl-butanedioic acid
ChEMBL
DrugBank
ZINC
PDB chain7rmp Chain D Residue 2103 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7rmp Allosteric role of the citrate synthase homology domain of ATP citrate lyase.
Resolution2.7 Å
Binding residue
(original residue number in PDB)
A280 A345 N346 F347 T348 R379 F533 S574 R576 I597 N638
Binding residue
(residue number reindexed from 1)
A279 A344 N345 F346 T347 R378 F471 S512 R514 I535 N576
Annotation score3
Enzymatic activity
Enzyme Commision number 2.3.3.8: ATP citrate synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0003878 ATP citrate synthase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0046912 acyltransferase activity, acyl groups converted into alkyl on transfer
Biological Process
GO:0006085 acetyl-CoA biosynthetic process
GO:0006101 citrate metabolic process
GO:0006107 oxaloacetate metabolic process
GO:0006629 lipid metabolic process
GO:0006633 fatty acid biosynthetic process
GO:0006695 cholesterol biosynthetic process
GO:0008610 lipid biosynthetic process
GO:0015936 coenzyme A metabolic process
Cellular Component
GO:0005576 extracellular region
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0035578 azurophil granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:7rmp, PDBe:7rmp, PDBj:7rmp
PDBsum7rmp
PubMed37076498
UniProtP53396|ACLY_HUMAN ATP-citrate synthase (Gene Name=ACLY)

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