Structure of PDB 8s5l Chain B Binding Site BS01

Receptor Information
>8s5l Chain B (length=507) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LWIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVR
INKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDT
IIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRT
PTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEIL
QQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPE
ELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQ
EGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWM
LQKGFLKEEDLTEKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEILREK
GFDQAPVVDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIR
LTDTLGRLSHILEMDHFALVVHEQIQYHSTGKSSQRQMVFGVVTAIDLLN
FVAAQER
Ligand information
Ligand IDHEM
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain8s5l Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8s5l Architecture and regulation of filamentous human cystathionine beta-synthase.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		S50 R51 C52 T53 P64 H65 A226 L230 Y233 R266
Binding residue
(residue number reindexed from 1)		S9 R10 C11 T12 P23 H24 A185 L189 Y192 R225
Annotation score1
Enzymatic activity
Enzyme Commision number 4.2.1.22: cystathionine beta-synthase.
Gene Ontology
Molecular Function
GO:0004122 cystathionine beta-synthase activity
GO:0005515 protein binding
GO:0016829 lyase activity
GO:0019825 oxygen binding
GO:0019899 enzyme binding
GO:0020037 heme binding
GO:0030170 pyridoxal phosphate binding
GO:0031625 ubiquitin protein ligase binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0050421 nitrite reductase (NO-forming) activity
GO:0070025 carbon monoxide binding
GO:0070026 nitric oxide binding
GO:0072341 modified amino acid binding
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0001958 endochondral ossification
GO:0001974 blood vessel remodeling
GO:0006534 cysteine metabolic process
GO:0006535 cysteine biosynthetic process from serine
GO:0006563 L-serine metabolic process
GO:0006565 L-serine catabolic process
GO:0006801 superoxide metabolic process
GO:0009069 serine family amino acid metabolic process
GO:0010749 regulation of nitric oxide mediated signal transduction
GO:0019343 cysteine biosynthetic process via cystathionine
GO:0019344 cysteine biosynthetic process
GO:0019346 transsulfuration
GO:0019448 L-cysteine catabolic process
GO:0021587 cerebellum morphogenesis
GO:0031667 response to nutrient levels
GO:0042262 DNA protection
GO:0043066 negative regulation of apoptotic process
GO:0043418 homocysteine catabolic process
GO:0044272 sulfur compound biosynthetic process
GO:0050667 homocysteine metabolic process
GO:0051593 response to folic acid
GO:0060135 maternal process involved in female pregnancy
GO:0060351 cartilage development involved in endochondral bone morphogenesis
GO:0070814 hydrogen sulfide biosynthetic process
GO:0071456 cellular response to hypoxia
GO:0097746 blood vessel diameter maintenance
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8s5l, PDBe:8s5l, PDBj:8s5l
PDBsum8s5l
PubMed38575566
UniProtP35520|CBS_HUMAN Cystathionine beta-synthase (Gene Name=CBS)

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