Structure of PDB 5kdt Chain B Binding Site BS01

Receptor Information
>5kdt Chain B (length=284) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSTRLKIVTIHQEPFVYVKPTLSDGTCKEEFTVNGDPVKKVICTGPNDTS
PGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNKK
EWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKGT
RITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYE
SAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGM
RKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQ
Ligand information
Ligand ID6RV
InChIInChI=1S/C16H8ClF6N5OS/c17-10-3-9(15(18,19)20)26-27(10)5-7-2-11(29)28-12(8-1-6(8)4-24)13(16(21,22)23)30-14(28)25-7/h2-3,6,8H,1,5H2/t6-,8+/m0/s1
InChIKeyFTIBNGABJNFFAI-POYBYMJQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5c1c(nn(c1Cl)CC2=CC(=O)N3C(=C(SC3=N2)C(F)(F)F)[C@@H]4C[C@H]4C#N)C(F)(F)F
CACTVS 3.385FC(F)(F)c1cc(Cl)n(CC2=CC(=O)N3C(=N2)SC(=C3[C@@H]4C[C@H]4C#N)C(F)(F)F)n1
OpenEye OEToolkits 2.0.5c1c(nn(c1Cl)CC2=CC(=O)N3C(=C(SC3=N2)C(F)(F)F)C4CC4C#N)C(F)(F)F
CACTVS 3.385FC(F)(F)c1cc(Cl)n(CC2=CC(=O)N3C(=N2)SC(=C3[CH]4C[CH]4C#N)C(F)(F)F)n1
FormulaC16 H8 Cl F6 N5 O S
Name(1~{R},2~{R})-2-[7-[[5-chloranyl-3-(trifluoromethyl)pyrazol-1-yl]methyl]-5-oxidanylidene-2-(trifluoromethyl)-[1,3]thiazolo[3,2-a]pyrimidin-3-yl]cyclopropane-1-carbonitrile
ChEMBLCHEMBL3799213
DrugBank
ZINC
PDB chain5kdt Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5kdt Discovery of GluN2A-Selective NMDA Receptor Positive Allosteric Modulators (PAMs): Tuning Deactivation Kinetics via Structure-Based Design.
Resolution2.44 Å
Binding residue
(original residue number in PDB)		K140 P141 Y144 H273
Binding residue
(residue number reindexed from 1)		K135 P136 Y139 H268
Annotation score1
Binding affinityBindingDB: EC50=6200nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0015276 ligand-gated monoatomic ion channel activity
Cellular Component
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:5kdt, PDBe:5kdt, PDBj:5kdt
PDBsum5kdt
PubMed26919761
UniProtQ05586|NMDZ1_HUMAN Glutamate receptor ionotropic, NMDA 1 (Gene Name=GRIN1)

[Back to BioLiP]