SMTL ID : 3hpt.2 (1 other biounit)

Crystal structure of human FxA in complex with (S)-2-cyano-1-(2-methylbenzofuran-5-yl)-3-(2-oxo-1-(2-oxo-2-(pyrrolidin-1-yl)ethyl)azepan-3-yl)guanidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-1-1-mer

Ligands

1 x YET: 1-cyano-2-(2-methyl-1-benzofuran-5-yl)-3-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]guanidine(Non-covalent)

YET.1: 19 residues within 4Å: Chain B: E.83, T.84, Y.85, E.135, F.162, D.179, A.180, C.181, Q.182, S.185, V.203, S.204, W.205, G.206, G.208, C.209, G.216, I.217, Y.218 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.85, B:V.203, B:Y.218 Hydrogen bonds: B:Q.182, B:Q.182, B:G.206, B:G.208, B:C.209 Water bridges: B:G.208, B:G.208, B:G.208

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain B: D.56, N.58, Q.61, E.62, E.63, E.66 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.56, B:N.58, B:Q.61, B:E.66, H2O.10

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain B: Y.173, D.174, R.211, K.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.214, B:K.214 Water bridges: B:Y.173

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: F.55, A.68 Chain B: L.109, P.110, L.225, D.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.69 GOL.5: 4 residues within 4Å: Chain B: R.79, T.81, D.86, F.87 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.79, B:T.81, B:D.86

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 6 residues within 4Å: Chain B: F.87, R.112, N.167, A.223, F.224, K.226 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.167 Water bridges: B:Q.166, B:K.226, B:K.226 Salt bridges: B:R.112, B:K.226

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 4 residues within 4Å: Chain B: Q.122, R.192, F.193, K.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.122, B:K.194 ACT.8: 4 residues within 4Å: Chain B: Y.173, D.174, T.175, K.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.174, B:T.175, B:K.176 ACT.9: 4 residues within 4Å: Chain B: F.35, Y.36, R.93, R.235 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.236 Salt bridges: B:R.93, B:R.235 ACT.11: 2 residues within 4Å: Chain B: R.49, F.50 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.50

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.10: 5 residues within 4Å: Chain B: G.4, Q.5, M.145, L.146, E.147 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Y. et al., Cyanoguanidine-based lactam derivatives as a novel class of orally bioavailable factor Xa inhibitors. Bioorg.Med.Chem.Lett. (2009)

Release Date

2009-11-17

Peptides

Coagulation factor X: A
Coagulation factor X: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Coagulation factor X

Coagulation factor X

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