Structure of PDB 4l8f Chain B Binding Site BS01

Receptor Information
>4l8f Chain B (length=287) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTNERPIIGVLAQDVFDPKPDRNSYIAASYVKFLESAGARVVPVMINKSE
DEYSRLFKSINGVLFPGGGVSLESSGYSKAAGIFYRLALEANSNGDYFPV
WGTALGFELLTLLTSGELLLSHTNTSGIALPLDFTEDVKGSRLFKEFPEE
LMKSLATEPLTENSHQWSITTENFTANKKLKKFYRVLSTNTDGYNKFVST
MEAYDFPIYATQWHPEKNAFEWTRPYIPHTPSAIKTTFYMANFFVNEARK
NLHSFASTEEEEKALIYNYKPEYTGIQSAFEQTYFFN
Ligand information
Ligand IDMTX
InChIInChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/t13-/m0/s1
InChIKeyFBOZXECLQNJBKD-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
CACTVS 3.341CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.5.0CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)NC(CCC(=O)O)C(=O)O
ACDLabs 10.04O=C(O)C(NC(=O)c1ccc(cc1)N(C)Cc2nc3c(nc2)nc(nc3N)N)CCC(=O)O
OpenEye OEToolkits 1.5.0CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
FormulaC20 H22 N8 O5
NameMETHOTREXATE
ChEMBLCHEMBL34259
DrugBankDB00563
ZINCZINC000001529323
PDB chain4l8f Chain B Residue 301 [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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PDB4l8f Structural insights into the hydrolysis and polymorphism of methotrexate polyglutamate by zebrafish gamma-glutamyl hydrolase
Resolution1.97 Å
Binding residue
(original residue number in PDB)		F20 G71 G72 G73 A108 L109 E112 S168 H169 Q170 W171 H218
Binding residue
(residue number reindexed from 1)		F16 G67 G68 G69 A104 L105 E108 S164 H165 Q166 W167 H214
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) A108 H218 E220
Catalytic site (residue number reindexed from 1) A104 H214 E216
Enzyme Commision number 3.4.19.9: folate gamma-glutamyl hydrolase.
Gene Ontology
Molecular Function
GO:0008242 omega peptidase activity
GO:0016787 hydrolase activity

View graph for
Molecular Function
External links
PDB RCSB:4l8f, PDBe:4l8f, PDBj:4l8f
PDBsum4l8f
PubMed24028568
UniProtQ6NY42

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