Structure of PDB 6nyy Chain B Binding Site BS03

Receptor Information
>6nyy Chain B (length=487) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGETTAKVLKDEIDVKFKDVAGCEEAKLEIMEFVNFLKNPKQYQDLGAKI
PKGAILTGPPGTGKTLLAKATAGEANVPFITVSGSEFLEMFVGVGPARVR
DLFALARKNAPCILFIDQIDAVGRKRGNFGGQSEQENTLNQLLVEMDGFN
TTTNVVILAGTNRPDILDPALLRPGRFDRQIFIGPPDIKGRASIFKVHLR
PLKLDSTLEKDKLARKLASLTPGFSGADVANVCNEAALIAARHLSDSINQ
KHFEQAIERVIGGLEKKTQVLQPEEKKTVAYHQAGHAVAGWYLEHADPLL
KVSIIPRGKGLGYAQYLPKEQYLYTKEQLLDRMCMTLGGRVSEEIFFGRI
TTGAQDDLRKVTQSAYAQIVQFGMNEKVGQISFDLPRQGDMVLEKPYSEA
TARLIDDEVRILINDAYKRTVALLTEKKADVEKVALLLLEKEVLDKNDMV
ELLGPRPFAEKSTYEEFVEGTGSLDEDTSLPEGLKDW
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain6nyy Chain B Residue 801 [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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PDB6nyy Unique Structural Features of the Mitochondrial AAA+ Protease AFG3L2 Reveal the Molecular Basis for Activity in Health and Disease.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		D309 V310 G351 T352 G353 K354 T355 L356 Q408 I486 H490 G518
Binding residue
(residue number reindexed from 1)		D19 V20 G61 T62 G63 K64 T65 L66 Q118 I194 H198 G226
Annotation score3
Enzymatic activity
Enzyme Commision number 3.4.24.-
3.6.-.-
Gene Ontology
Molecular Function
GO:0004176 ATP-dependent peptidase activity
GO:0004222 metalloendopeptidase activity
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0016020 membrane

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:6nyy, PDBe:6nyy, PDBj:6nyy
PDBsum6nyy
PubMed31327635
UniProtQ9Y4W6|AFG32_HUMAN Mitochondrial inner membrane m-AAA protease component AFG3L2 (Gene Name=AFG3L2)

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