Structure of PDB 5jd7 Chain A Binding Site BS01

Receptor Information

>5jd7 Chain A (length=127) Species: 9606 (Homo sapiens)

IKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGARGD
TFFIISKGTVNVTREDEDPVFLRTLGKGDWFGEKALQGEDVRTANVIAAE
AVTCLVIDRDSFKHLIGGLDDVSNKAY

Ligand information

• Ligand ID: 6JR
• InChI: InChI=1S/C18H16N5O7P/c24-13-14-11(7-28-31(26,27)30-14)29-17(13)23-8-19-12-15(23)21-18-20-10(6-22(18)16(12)25)9-4-2-1-3-5-9/h1-6,8,11,13-14,17,24H,7H2,(H,20,21)(H,26,27)/t11-,13-,14-,17-/m1/s1
• InChIKey: TVSIKYJKUPRIDV-LSCFUAHRSA-N
• SMILES:
  CACTVS 3.385: O[C@@H]1[C@@H]2O[P](O)(=O)OC[C@H]2O[C@H]1n3cnc4C(=O)n5cc(nc5Nc34)c6ccccc6
  CACTVS 3.385: O[CH]1[CH]2O[P](O)(=O)OC[CH]2O[CH]1n3cnc4C(=O)n5cc(nc5Nc34)c6ccccc6
  OpenEye OEToolkits 2.0.4: c1ccc(cc1)c2cn3c(n2)Nc4c(ncn4C5C(C6C(O5)COP(=O)(O6)O)O)C3=O
  OpenEye OEToolkits 2.0.4: c1ccc(cc1)c2cn3c(n2)Nc4c(ncn4[C@H]5[C@@H]([C@H]6[C@H](O5)COP(=O)(O6)O)O)C3=O
  ACDLabs 12.01: n54C(c3ncn(C2OC1COP(OC1C2O)(O)=O)c3Nc4nc(c5)c6ccccc6)=O
• Formula: C18 H16 N5 O7 P
• Name: 3-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-6-phenyl-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one;
  PET-cGMP
• ZINC: ZINC000101148330
• PDB chain: 5jd7 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jd7 Structural Basis of Analog Specificity in PKG I and II.
• Resolution: 1.749 Å
• Binding residue (original residue number in PDB): V283 R285 L296 R297 F305 G306 E307 K308 A309 R316 T317 A318 V320 Y351
• Binding residue (residue number reindexed from 1): V62 R64 L72 R73 F81 G82 E83 K84 A85 R92 T93 A94 V96 Y127
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.11.12: cGMP-dependent protein kinase.

Gene Ontology

Molecular Function

• GO:0004692 cGMP-dependent protein kinase activity
• GO:0005524 ATP binding

External links

• PDB: RCSB:5jd7, PDBe:5jd7, PDBj:5jd7
• PDBsum: 5jd7
• PubMed: 28793191
• UniProt: Q13976|KGP1_HUMAN cGMP-dependent protein kinase 1 (Gene Name=PRKG1)