Structure of PDB 7ndz Chain C Binding Site BS03

Receptor Information
>7ndz Chain C (length=217) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMDEERDRHLIEYLMKHG
HETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPS
PERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPL
NLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTF
EAFLKYAYKGDILKEVQ
Ligand information
Ligand IDHUF
InChIInChI=1S/C28H35N9O16P2/c1-11-3-13-14(4-12(11)2)37(10-38)19-25(33-28(45)34-26(19)44)35(13)5-15(39)20(41)16(40)6-50-54(46,47)53-55(48,49)51-7-17-21(42)22(43)27(52-17)36-9-32-18-23(29)30-8-31-24(18)36/h3-4,8-10,15-17,20-22,27,39-43H,5-7H2,1-2H3,(H,46,47)(H,48,49)(H2,29,30,31)(H2,33,34,44,45)/t15-,16+,17+,20-,21+,22+,27+/m0/s1
InChIKeyKZQASMOVHMAAKH-MZWSMYJRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc2N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C6=C(N(C=O)c2cc1C)C(=O)NC(=O)N6
OpenEye OEToolkits 2.0.7Cc1cc2c(cc1C)N(C3=C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C=O
OpenEye OEToolkits 2.0.7Cc1cc2c(cc1C)N(C3=C(N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C=O
CACTVS 3.385Cc1cc2N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C6=C(N(C=O)c2cc1C)C(=O)NC(=O)N6
FormulaC28 H35 N9 O16 P2
Name[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain7ndz Chain C Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7ndz An enzymatic activation of formaldehyde for nucleotide methylation.
Resolution2.7 Å
Binding residue
(original residue number in PDB)
R78 H79 R80 I81 N169 L173 R174 H178
Binding residue
(residue number reindexed from 1)
R76 H77 R78 I79 N167 L171 R172 H176
Annotation score2
Enzymatic activity
Enzyme Commision number 2.1.1.148: thymidylate synthase (FAD).
Gene Ontology
Molecular Function
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0050797 thymidylate synthase (FAD) activity
GO:0070402 NADPH binding
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0032259 methylation

View graph for
Molecular Function

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Biological Process
External links
PDB RCSB:7ndz, PDBe:7ndz, PDBj:7ndz
PDBsum7ndz
PubMed34315871
UniProtQ9WYT0|THYX_THEMA Flavin-dependent thymidylate synthase (Gene Name=thyX)

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