Structure of PDB 6lpp Chain A Binding Site BS01

Receptor Information
>6lpp Chain A (length=466) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRRLPFSTVSKQDLAAFERIVPGGVVTDPEALQAPNVDWLRTLRGCSKVL
LRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTARM
NRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGGN
VATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQ
LFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGML
GEILSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLIETSGSNAGHDAEK
LGHFLEHALGSGLVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKYD
LSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNVTAEAFSPSL
LAALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKA
LLDPKGILNPYKTLPS
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain6lpp Chain A 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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PDB6lpp Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		W92 P128 G130 G131 N132 T133 G134 M135 G138 S139 L192 G193 A194 C198 G202 N203 A205 T206 A208 G210 G260 I265 E475 H476
Binding residue
(residue number reindexed from 1)		W39 P75 G77 G78 N79 T80 G81 M82 G85 S86 L139 G140 A141 C145 G149 N150 A152 T153 A155 G157 G207 I212 E422 H423
Annotation score1
Enzymatic activity
Enzyme Commision number 1.1.99.39: D-2-hydroxyglutarate dehydrogenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008270 zinc ion binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
GO:0051990 (R)-2-hydroxyglutarate dehydrogenase activity
GO:0071949 FAD binding
Biological Process
GO:0006103 2-oxoglutarate metabolic process
GO:0006108 malate metabolic process
GO:0010042 response to manganese ion
GO:0010043 response to zinc ion
GO:0019538 protein metabolic process
GO:0032025 response to cobalt ion
GO:0032026 response to magnesium ion
GO:0051592 response to calcium ion
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:6lpp, PDBe:6lpp, PDBj:6lpp
PDBsum6lpp
PubMed33431826
UniProtQ8N465|D2HDH_HUMAN D-2-hydroxyglutarate dehydrogenase, mitochondrial (Gene Name=D2HGDH)

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