SMTL ID : 5qtw.1

FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl (2R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-14-[(methoxycarbonyl)amino]-2,3,4,5,6,7-hexahydro-1H-8,11-epimino-1,9-benzodiazacyclotridecine-2-carboxylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

monomer

Ligands

1 x QLM: methyl (2R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-14-[(methoxycarbonyl)amino]-2,3,4,5,6,7-hexahydro-1H-8,11-epimino-1,9-benzodiazacyclotridecine-2-carboxylate(Non-covalent)

QLM.1: 31 residues within 4Å: Chain A: R.26, H.27, L.28, C.29, H.44, C.45, Y.134, L.137, I.141, D.182, A.183, C.184, K.185, G.186, D.187, S.188, T.206, S.207, W.208, G.209, E.210, G.211, C.212, G.219, V.220, Y.221 Ligands: EDO.4, EDO.7, EDO.8, EDO.10, EDO.17 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.141, A:T.206 Hydrogen bonds: A:H.27, A:L.28, A:K.185, A:G.186, A:D.187, A:S.188, A:S.188 Water bridges: A:L.28, A:H.44, A:G.209 Salt bridges: A:R.26

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 10 residues within 4Å: Chain A: S.7, V.8, R.9, G.10, E.11, W.12, P.13, I.61, L.62, L.145 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.10, A:E.11, A:W.12, A:W.12, A:I.61 Water bridges: A:I.61 SO4.3: 2 residues within 4Å: Chain A: R.161, R.177 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.161, A:R.177

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Ligands: QLM.1, EDO.7, EDO.8, EDO.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.185 EDO.5: 5 residues within 4Å: Chain A: N.36, T.102, V.103, G.104, Y.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.36, A:Y.105 EDO.6: 2 residues within 4Å: Chain A: R.9, L.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.9 Water bridges: A:N.63 EDO.7: 8 residues within 4Å: Chain A: L.137, K.185, G.209, E.210, G.211 Ligands: QLM.1, EDO.4, EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.209, A:G.211 Water bridges: A:K.185, A:K.185 EDO.8: 7 residues within 4Å: Chain A: E.89, W.208, G.209, E.210 Ligands: QLM.1, EDO.4, EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.210 Water bridges: A:G.209, A:G.209 EDO.9: 2 residues within 4Å: Chain A: T.168, H.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.169 EDO.10: 2 residues within 4Å: Chain A: R.26 Ligands: QLM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.26 EDO.11: 3 residues within 4Å: Chain A: Q.25, I.67, K.68 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.19, A:Q.25, A:H.27, A:K.68 EDO.12: 9 residues within 4Å: Chain A: V.153, E.157, R.161, G.175, Y.176, R.177, E.216, R.217, P.218 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.157, A:E.157, A:R.161, A:Y.176 Water bridges: A:R.217 EDO.13: 5 residues within 4Å: Chain A: V.153, H.169, M.171, I.172, N.223 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.169, A:N.223 Water bridges: A:V.153, A:N.155, A:N.155 EDO.14: 6 residues within 4Å: Chain A: S.90, G.91, Y.92, T.168, K.170, M.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.90, A:Y.92, A:T.168 EDO.15: 4 residues within 4Å: Chain A: E.11, W.12, W.128, K.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.147 Water bridges: A:W.200 EDO.16: 6 residues within 4Å: Chain A: I.34, G.35, W.38, L.232, T.235, Q.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.235 Water bridges: A:N.36, A:N.36 EDO.17: 2 residues within 4Å: Ligands: QLM.1, EDO.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.185, A:K.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fang, T. et al., Orally bioavailable amine-linked macrocyclic inhibitors of factor XIa. Bioorg.Med.Chem.Lett. (2020)

Release Date

2020-01-29

Peptides

Coagulation factor XI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Coagulation factor XI

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