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

Crystal structure of human FXA in complex with methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}acrylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ENS: methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}acrylate(Non-covalent)

ENS.1: 17 residues within 4Å: Chain B: E.83, T.84, Y.85, R.132, E.135, F.162, D.179, A.180, C.181, Q.182, V.203, W.205, G.206, G.208, C.209, G.216, I.217 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.85, B:V.203 Hydrogen bonds: B:Q.182, B:G.206, B:G.206, B:G.208, B:G.208 Water bridges: B:G.206

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain B: D.56, N.58, Q.61, E.66 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.56, B:N.58, B:Q.61, B:E.66

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

NA.3: 7 residues within 4Å: Chain B: Y.173, D.174, T.175, K.176, A.210, R.211, K.214 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.210

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

MES.4: 7 residues within 4Å: Chain B: F.87, R.112, Q.166, N.167, A.223, F.224, K.226 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.167 Water bridges: B:K.226, B:W.227, B:R.230 Salt bridges: B:R.112, B:K.226

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: A.68, R.69 Chain B: L.109, P.110, L.225, D.229 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.109, A:R.69 Water bridges: B:L.109, B:R.112, B:D.229, B:D.229 GOL.6: 3 residues within 4Å: Chain B: R.79, T.81, D.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.79, B:D.86, B:D.86 GOL.7: 3 residues within 4Å: Chain B: V.73, V.74, I.75 2 PLIP interactions: 2 interactions with chain B Water bridges: B:V.74, B:V.74

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Y. et al., Design, Structure-Activity Relationships, X-ray Crystal Structure, and Energetic Contributions of a Critical P1 Pharmacophore: 3-Chloroindole-7-yl-Based Factor Xa Inhibitors. J.Med.Chem. (2008)

Release Date

2008-12-30

Peptides

Factor X light chain: A
Activated factor Xa heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Factor X light chain

Activated factor Xa heavy chain

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