SMTL ID : 1mq5.1

Crystal Structure of 3-chloro-N-[4-chloro-2-[[(4-chlorophenyl)amino]carbonyl]phenyl]-4-[(4-methyl-1-piperazinyl)methyl]-2-thiophenecarboxamide Complexed with Human Factor Xa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

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

1 x XLC: 3-CHLORO-N-[4-CHLORO-2-[[(4-CHLOROPHENYL)AMINO]CARBONYL]PHENYL]-4-[(4-METHYL-1-PIPERAZINYL)METHYL]-2-THIOPHENECARBOXAMIDE(Non-covalent)

XLC.2: 20 residues within 4Å: Chain A: K.82, E.83, Y.85, R.132, E.135, F.162, D.179, A.180, C.181, Q.182, V.203, S.204, W.205, G.206, E.207, G.208, C.209, G.216, I.217, Y.218 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.182, A:V.203, A:W.205 Hydrogen bonds: A:Q.182, A:G.206, A:G.208, A:G.208 Salt bridges: A:E.83 pi-Stacking: A:F.162 Halogen bonds: A:R.132, A:E.135

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: L.32, S.33, E.34, F.100, P.106 Chain B: Y.44 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.46, A:E.34 Water bridges: B:P.43 GOL.4: 4 residues within 4Å: Chain A: L.109, P.110, L.225 Chain B: R.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.27 Water bridges: B:R.27 GOL.5: 5 residues within 4Å: Chain A: W.114, S.117 Chain B: C.14, H.15, E.16 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.117, A:S.117, B:E.16 Water bridges: A:D.113, A:W.114, A:W.114, A:S.117, A:T.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adler, M. et al., Crystal Structures of Two Potent Nonamidine Inhibitors Bound to Factor Xa. Biochemistry (2002)

Release Date

2003-01-28

Peptides

COAGULATION FACTOR X HEAVY CHAIN: A
COAGULATION FACTOR X LIGHT CHAIN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

COAGULATION FACTOR X HEAVY CHAIN

COAGULATION FACTOR X LIGHT CHAIN

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