Structure of PDB 1y60 Chain A Binding Site BS01

Receptor Information
>1y60 Chain A (length=168) Species: 272630 (Methylorubrum extorquens AM1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKITKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTS
LLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAE
GIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPK
ASVVTEQRKSATHPFAAN
Ligand information
Ligand IDH4M
InChIInChI=1S/C31H45N6O16P/c1-13-22-14(2)36(12-37(22)23-27(33-13)34-31(32)35-28(23)45)16-5-3-15(4-6-16)9-17(38)24(42)18(39)10-50-30-26(44)25(43)20(52-30)11-51-54(48,49)53-19(29(46)47)7-8-21(40)41/h3-6,13-14,17-20,22,24-26,30,38-39,42-44H,7-12H2,1-2H3,(H,40,41)(H,46,47)(H,48,49)(H4,32,33,34,35,45)/t13-,14+,17-,18+,19?,20+,22+,24-,25+,26+,30-/m0/s1
InChIKeyGBMIGEWJAPFSQI-UQXKJNEMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H]1NC2=C(N3CN([C@H](C)[C@@H]13)c4ccc(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]5O[C@H](CO[P](O)(=O)OC(CCC(O)=O)C(O)=O)[C@@H](O)[C@H]5O)cc4)C(=O)NC(=N2)N
ACDLabs 12.01N1=C(N)NC(C2=C1NC(C3N2CN(C3C)c4ccc(cc4)CC(C(O)C(O)COC5OC(COP(=O)(O)OC(CCC(=O)O)C(=O)O)C(O)C5O)O)C)=O
CACTVS 3.385C[CH]1NC2=C(N3CN([CH](C)[CH]13)c4ccc(C[CH](O)[CH](O)[CH](O)CO[CH]5O[CH](CO[P](O)(=O)OC(CCC(O)=O)C(O)=O)[CH](O)[CH]5O)cc4)C(=O)NC(=N2)N
OpenEye OEToolkits 1.7.6CC1C2C(N(CN2C3=C(N1)N=C(NC3=O)N)c4ccc(cc4)CC(C(C(COC5C(C(C(O5)COP(=O)(O)OC(CCC(=O)O)C(=O)O)O)O)O)O)O)C
OpenEye OEToolkits 1.7.6C[C@H]1[C@@H]2[C@H](N(CN2C3=C(N1)N=C(NC3=O)N)c4ccc(cc4)C[C@@H]([C@@H](C(CO[C@@H]5[C@@H]([C@@H]([C@H](O5)COP(=O)(O)OC(CCC(=O)O)C(=O)O)O)O)O)O)O)C
FormulaC31 H45 N6 O16 P
Name5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN
ChEMBL
DrugBank
ZINC
PDB chain1y60 Chain B Residue 998 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1y60 How an enzyme binds the C1-carrier tetrahydromethanopterin: Structure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1
Resolution1.9 Å
Binding residue
(original residue number in PDB)		H22 D24 K71 V72 T73 F119 F166
Binding residue
(residue number reindexed from 1)		H21 D23 K70 V71 T72 F118 F165
Annotation score4
Enzymatic activity
Enzyme Commision number 4.2.1.147: 5,6,7,8-tetrahydromethanopterin hydro-lyase.
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0016840 carbon-nitrogen lyase activity
Biological Process
GO:0006730 one-carbon metabolic process
GO:0009636 response to toxic substance
GO:0016051 carbohydrate biosynthetic process
GO:0046294 formaldehyde catabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1y60, PDBe:1y60, PDBj:1y60
PDBsum1y60
PubMed15632161
UniProtQ9FA38|FAE_METEA 5,6,7,8-tetrahydromethanopterin hydro-lyase (Gene Name=fae)

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