Structure of PDB 6lpn Chain B Binding Site BS01

Receptor Information
>6lpn Chain B (length=467) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVRRLPFSTVSKQDLAAFERIVPGGVVTDPEALQAPNVDWLRTLRGCSKV
LLRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTAR
MNRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGG
NVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLK
QLFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGM
LGEILSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLIETSGSNAGHDAE
KLGHFLEHALGSGLVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKY
DLSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNVTAEAFSPS
LLAALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLK
ALLDPKGILNPYKTLPS
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 chain6lpn 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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PDB6lpn Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.
Resolution2.206 Å
Binding residue
(original residue number in PDB)		W92 P128 G130 G131 N132 T133 G134 M135 G138 S139 L192 A194 C198 H199 G202 N203 A205 T206 G260 I264 I265 E475 N512
Binding residue
(residue number reindexed from 1)		W40 P76 G78 G79 N80 T81 G82 M83 G86 S87 L140 A142 C146 H147 G150 N151 A153 T154 G208 I212 I213 E423 N460
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6lpn, PDBe:6lpn, PDBj:6lpn
PDBsum6lpn
PubMed33431826
UniProtQ8N465|D2HDH_HUMAN D-2-hydroxyglutarate dehydrogenase, mitochondrial (Gene Name=D2HGDH)

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