Structure of PDB 3qxt Chain A Binding Site BS01

Receptor Information
>3qxt Chain A (length=124) Species: 9844 (Lama glama) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVQLVESGGGLVQAGGSLRLSCAASRRSSRSWAMAWFRQAPGKEREFVAK
ISGDGRLTTYGDSVKGRFTISRDKGKNTVYLQMDSLKPEDTAVYYCAADD
NYVTASWRSGPDYWGQGTQVTVSS
Ligand information
Ligand IDMTX
InChIInChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/t13-/m0/s1
InChIKeyFBOZXECLQNJBKD-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
CACTVS 3.341CN(Cc1cnc2nc(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
OpenEye OEToolkits 1.5.0CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)NC(CCC(=O)O)C(=O)O
ACDLabs 10.04O=C(O)C(NC(=O)c1ccc(cc1)N(C)Cc2nc3c(nc2)nc(nc3N)N)CCC(=O)O
OpenEye OEToolkits 1.5.0CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
FormulaC20 H22 N8 O5
NameMETHOTREXATE
ChEMBLCHEMBL34259
DrugBankDB00563
ZINCZINC000001529323
PDB chain3qxt Chain A Residue 2000 [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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PDB3qxt An anti-hapten camelid antibody reveals a cryptic binding site with significant energetic contributions from a nonhypervariable loop.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		V4 A26 R28 R29 S30 R32 W34 M36 R74 N79 T80 V81
Binding residue
(residue number reindexed from 1)		V2 A24 R26 R27 S28 R30 W32 M34 R72 N77 T78 V79
Annotation score1
Binding affinityMOAD: Kd=6700nM
PDBbind-CN: -logKd/Ki=5.22,Kd=6uM
External links