0.017655
0.000000
0.000000
0.000000
0.013644
0.000000
0.000000
0.000000
0.012655
0.00000
0.00000
0.00000
Adler, M.
Whitlow, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
56.640
73.290
79.020
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
Ca 2
40.078
CALCIUM ION
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
C23 H20 Cl3 N5 O4 S
568.860
3-CHLORO-N-[4-CHLORO-2-[[(5-CHLORO-2-PYRIDINYL)AMINO]CARBONYL]-6-METHOXYPHENYL]-4-[[(4,5-DIHYDRO-2-OXAZOLYL)METHYLAMINO]METHYL]-2-THIOPHENECARBOXAMIDE
non-polymer
US
Biochemistry
BICHAW
0033
0006-2960
41
15514
15523
10.1021/bi0264061
12501180
Crystal Structures of Two Potent Nonamidine Inhibitors Bound to Factor Xa
2002
US
Biochemistry
BICHAW
0033
0006-2960
39
12534
12542
10.1021/bi001477q
Preparation, Characterization and the Crystal Structure of the Inhibitor Zk-807834 (Ci-1031) Complexed with Factor Xa
2000
US
J.Med.Chem.
JMCMAR
0151
0022-2623
43
3226
3232
10.1021/jm000940u
Crystal Structures of Human Factor Xa Complexed with Potent Inhibitors
2000
US
J.Med.Chem.
JMCMAR
0151
0022-2623
41
3557
3562
10.1021/jm980280h
Discovery of N-[2-[5-[Amino(imino)methyl]-2-hydroxyphenoxy]-3,5-difluoro-
6-[3-(4,5-dihydro-1-methyl-1H-imidazol-2-yl)phenoxy]pyridin-4-yl]-N-methylglycine (ZK-807834):
A Potent, Selective, and Orally Active Inhibitor of the Blood Coagulation Enzyme Factor Xa
1998
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
CCD
2000-05-30
ADSC QUANTUM 4
SI(111)
SINGLE WAVELENGTH
M
x-ray
1
1.033
1.0
BL9-2
SSRL
1.033
1.033
SYNCHROTRON
SSRL BEAMLINE BL9-2
26346.000
COAGULATION FACTOR X HEAVY CHAIN
3.4.21.6
CATALYTIC DOMAIN
1
nat
polymer
5460.121
COAGULATION FACTOR X LIGHT CHAIN
3.4.21.6
EPIDERMAL GROWTH FACTOR LIKE DOMAIN 2
1
nat
polymer
40.078
CALCIUM ION
1
syn
non-polymer
568.860
3-CHLORO-N-[4-CHLORO-2-[[(5-CHLORO-2-PYRIDINYL)AMINO]CARBONYL]-6-METHOXYPHENYL]-4-[[(4,5-DIHYDRO-2-OXAZOLYL)METHYLAMINO]METHYL]-2-THIOPHENECARBOXAMIDE
1
syn
non-polymer
92.094
GLYCEROL
3
syn
non-polymer
18.015
water
164
nat
water
stuart factor
stuart factor
no
no
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRF
TKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSS
SFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMK
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRF
TKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSS
SFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMK
A
polypeptide(L)
no
no
KLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTL
KLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTL
L
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
EXTRACTED FROM BLOOD
Homo
sample
9606
Homo sapiens
human
EXTRACTED FROM BLOOD
Homo
sample
9606
Homo sapiens
1
2.44
51.2
VAPOR DIFFUSION, HANGING DROP
7.50
A THREE-FOLD EXCESS OF A PROPRIETARY FACTOR XA INHIBITOR WITH PICOMOLAR AFFINITY WAS
ADDED TO THE DES-GLA-FACTOR XA. THIS INHIBITOR IS BASED
ON THE SAME TEMPLATE AS XLD IN 1MQ6. THE PROTEIN WAS THEN
CONCENTRATED TO 12-17 MG/ML. CRYSTALS WERE GROWN USING 2 UL
OF COMPLEX WITH 2 UL OF RESERVOIR CONTAINING 15-21% PEG1500
AND 10 MM CACL2. 30-40 UL SITTING DROPS CONTAINING
SATURATED INHIBITOR (5 MM) IN 21% PEG1500, 5 MM CACL2, 20
MM NACL, 25 MM TRIS PH 7.5 (CRYSTAL SOAKING SOLUTION)
WERE EQUILIBRATED OVER A 1 ML RESERVOIR CONTAINING THE
CRYSTAL SOAKING SOLUTION FOR 1 TO 2 DAYS. A SINGLE FACTOR
XA CRYSTAL WAS TRANSFERRED USING A MOUNTED CRYOLOOP INTO ONE
OF THESE SITTING DROPS AND ALLOWED TO SOAK FOR THREE OR MORE
DAYS. AFTER THE INITIAL SOAK, EACH CRYSTAL WAS THEN
TRANSFERRED TO AN UNUSED DROP AND ALLOWED TO SOAK FOR SECOND
PERIOD OF THREE OR MORE DAYS. pH 7.50, VAPOR DIFFUSION, HANGING DROP,
temperature 293K
293
pdbx_unobs_or_zero_occ_atoms
software
repository
Initial release
Version format compliance
Non-polymer description
Version format compliance
Advisory
Refinement description
1
0
2003-01-28
1
1
2008-04-28
1
2
2011-07-13
1
3
2017-10-11
_software.name
FACTOR XA COMPLEXED TO ZK807834
FACTOR XA COMPLEXED TO RPR128515
FACTOR XA COMPLEXED TO RPR208707
FACTOR XA COMPLEXED TO RPR208815
TRYSPIN COMPLEXED TO FACTOR XA INHIBITOR
TRYSPIN COMPLEXED TO FACTOR XA INHIBITOR
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
BIOMOLECULE: 1
THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC
ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S).
FACTOR XA FORMS A COMPLEX WITH FACTOR VA IN
THE PRESENCE OF CALCIUM AND A PHOSPHOLIPID
MEMBRANE TO PRODUCE THE PROTHROMBINASE COMPLEX.
THIS ENTRY CONTAINS THE EPIDERMAL GROWTH FACTOR
LIKE DOMAIN 2(L) AND THE CATALYTIC DOMAIN (A)
OF FACTOR XA IN THE CRYSTALLOGRAPHIC ASYMMETRIC
UNIT. THE COORDINATES DO NOT CONTAIN THE GLA
DOMAIN OR THE EPIDERMAL GROWTH FACTOR LIKE DOMAIN
1 OF FACTOR XA. ALTHOUGH THE ASYMMETRIC UNIT
CONTAINS A FUNCTIONAL PROTEASE, IT DOES HAVE THE
SAME SPECIFICITY AS THE PROTHROMBINASE COMPLEX.
SEE REMARK 350 FOR INFORMATION ON GENERATING THE
BIOLOGICAL MOLECULE(S).
RCSB
Y
RCSB
2002-09-13
REL
REL
CA
CALCIUM ION
XLD
3-CHLORO-N-[4-CHLORO-2-[[(5-CHLORO-2-PYRIDINYL)AMINO]CARBONYL]-6-METHOXYPHENYL]-4-[[(4,5-DIHYDRO-2-OXAZOLYL)METHYLAMINO]METHYL]-2-THIOPHENECARBOXAMIDE
GOL
GLYCEROL
HOH
water
CA
501
3
CA
CA
501
A
LIG
500
4
XLD
XLD
500
A
GOL
502
5
GOL
GOL
502
A
GOL
503
5
GOL
GOL
503
A
GOL
504
5
GOL
GOL
504
A
HOH
600
6
HOH
HOH
600
A
HOH
601
6
HOH
HOH
601
A
HOH
602
6
HOH
HOH
602
A
HOH
603
6
HOH
HOH
603
A
HOH
604
6
HOH
HOH
604
A
HOH
605
6
HOH
HOH
605
A
HOH
606
6
HOH
HOH
606
A
HOH
607
6
HOH
HOH
607
A
HOH
609
6
HOH
HOH
609
A
HOH
610
6
HOH
HOH
610
A
HOH
611
6
HOH
HOH
611
A
HOH
612
6
HOH
HOH
612
A
HOH
613
6
HOH
HOH
613
A
HOH
614
6
HOH
HOH
614
A
HOH
615
6
HOH
HOH
615
A
HOH
618
6
HOH
HOH
618
A
HOH
619
6
HOH
HOH
619
A
HOH
620
6
HOH
HOH
620
A
HOH
621
6
HOH
HOH
621
A
HOH
622
6
HOH
HOH
622
A
HOH
624
6
HOH
HOH
624
A
HOH
625
6
HOH
HOH
625
A
HOH
626
6
HOH
HOH
626
A
HOH
627
6
HOH
HOH
627
A
HOH
628
6
HOH
HOH
628
A
HOH
629
6
HOH
HOH
629
A
HOH
630
6
HOH
HOH
630
A
HOH
631
6
HOH
HOH
631
A
HOH
632
6
HOH
HOH
632
A
HOH
633
6
HOH
HOH
633
A
HOH
634
6
HOH
HOH
634
A
HOH
635
6
HOH
HOH
635
A
HOH
636
6
HOH
HOH
636
A
HOH
637
6
HOH
HOH
637
A
HOH
638
6
HOH
HOH
638
A
HOH
639
6
HOH
HOH
639
A
HOH
640
6
HOH
HOH
640
A
HOH
641
6
HOH
HOH
641
A
HOH
642
6
HOH
HOH
642
A
HOH
644
6
HOH
HOH
644
A
HOH
645
6
HOH
HOH
645
A
HOH
647
6
HOH
HOH
647
A
HOH
648
6
HOH
HOH
648
A
HOH
649
6
HOH
HOH
649
A
HOH
651
6
HOH
HOH
651
A
HOH
654
6
HOH
HOH
654
A
HOH
655
6
HOH
HOH
655
A
HOH
657
6
HOH
HOH
657
A
HOH
658
6
HOH
HOH
658
A
HOH
660
6
HOH
HOH
660
A
HOH
661
6
HOH
HOH
661
A
HOH
662
6
HOH
HOH
662
A
HOH
663
6
HOH
HOH
663
A
HOH
664
6
HOH
HOH
664
A
HOH
665
6
HOH
HOH
665
A
HOH
666
6
HOH
HOH
666
A
HOH
667
6
HOH
HOH
667
A
HOH
669
6
HOH
HOH
669
A
HOH
670
6
HOH
HOH
670
A
HOH
671
6
HOH
HOH
671
A
HOH
672
6
HOH
HOH
672
A
HOH
673
6
HOH
HOH
673
A
HOH
674
6
HOH
HOH
674
A
HOH
675
6
HOH
HOH
675
A
HOH
677
6
HOH
HOH
677
A
HOH
678
6
HOH
HOH
678
A
HOH
679
6
HOH
HOH
679
A
HOH
680
6
HOH
HOH
680
A
HOH
681
6
HOH
HOH
681
A
HOH
682
6
HOH
HOH
682
A
HOH
683
6
HOH
HOH
683
A
HOH
684
6
HOH
HOH
684
A
HOH
685
6
HOH
HOH
685
A
HOH
686
6
HOH
HOH
686
A
HOH
687
6
HOH
HOH
687
A
HOH
688
6
HOH
HOH
688
A
HOH
691
6
HOH
HOH
691
A
HOH
693
6
HOH
HOH
693
A
HOH
694
6
HOH
HOH
694
A
HOH
696
6
HOH
HOH
696
A
HOH
697
6
HOH
HOH
697
A
HOH
698
6
HOH
HOH
698
A
HOH
699
6
HOH
HOH
699
A
HOH
700
6
HOH
HOH
700
A
HOH
701
6
HOH
HOH
701
A
HOH
702
6
HOH
HOH
702
A
HOH
703
6
HOH
HOH
703
A
HOH
704
6
HOH
HOH
704
A
HOH
705
6
HOH
HOH
705
A
HOH
706
6
HOH
HOH
706
A
HOH
707
6
HOH
HOH
707
A
HOH
708
6
HOH
HOH
708
A
HOH
709
6
HOH
HOH
709
A
HOH
710
6
HOH
HOH
710
A
HOH
711
6
HOH
HOH
711
A
HOH
712
6
HOH
HOH
712
A
HOH
713
6
HOH
HOH
713
A
HOH
714
6
HOH
HOH
714
A
HOH
715
6
HOH
HOH
715
A
HOH
716
6
HOH
HOH
716
A
HOH
717
6
HOH
HOH
717
A
HOH
718
6
HOH
HOH
718
A
HOH
719
6
HOH
HOH
719
A
HOH
720
6
HOH
HOH
720
A
HOH
721
6
HOH
HOH
721
A
HOH
722
6
HOH
HOH
722
A
HOH
724
6
HOH
HOH
724
A
HOH
726
6
HOH
HOH
726
A
HOH
727
6
HOH
HOH
727
A
HOH
732
6
HOH
HOH
732
A
HOH
734
6
HOH
HOH
734
A
HOH
735
6
HOH
HOH
735
A
HOH
736
6
HOH
HOH
736
A
HOH
738
6
HOH
HOH
738
A
HOH
739
6
HOH
HOH
739
A
HOH
740
6
HOH
HOH
740
A
HOH
742
6
HOH
HOH
742
A
HOH
743
6
HOH
HOH
743
A
HOH
746
6
HOH
HOH
746
A
HOH
747
6
HOH
HOH
747
A
HOH
748
6
HOH
HOH
748
A
HOH
749
6
HOH
HOH
749
A
HOH
750
6
HOH
HOH
750
A
HOH
753
6
HOH
HOH
753
A
HOH
754
6
HOH
HOH
754
A
HOH
755
6
HOH
HOH
755
A
HOH
756
6
HOH
HOH
756
A
HOH
757
6
HOH
HOH
757
A
HOH
758
6
HOH
HOH
758
A
HOH
759
6
HOH
HOH
759
A
HOH
760
6
HOH
HOH
760
A
HOH
761
6
HOH
HOH
761
A
HOH
762
6
HOH
HOH
762
A
HOH
608
6
HOH
HOH
608
L
HOH
616
6
HOH
HOH
616
L
HOH
617
6
HOH
HOH
617
L
HOH
623
6
HOH
HOH
623
L
HOH
643
6
HOH
HOH
643
L
HOH
646
6
HOH
HOH
646
L
HOH
650
6
HOH
HOH
650
L
HOH
652
6
HOH
HOH
652
L
HOH
653
6
HOH
HOH
653
L
HOH
656
6
HOH
HOH
656
L
HOH
659
6
HOH
HOH
659
L
HOH
668
6
HOH
HOH
668
L
HOH
676
6
HOH
HOH
676
L
HOH
689
6
HOH
HOH
689
L
HOH
690
6
HOH
HOH
690
L
HOH
692
6
HOH
HOH
692
L
HOH
695
6
HOH
HOH
695
L
HOH
723
6
HOH
HOH
723
L
HOH
725
6
HOH
HOH
725
L
HOH
728
6
HOH
HOH
728
L
HOH
729
6
HOH
HOH
729
L
HOH
730
6
HOH
HOH
730
L
HOH
731
6
HOH
HOH
731
L
HOH
733
6
HOH
HOH
733
L
HOH
737
6
HOH
HOH
737
L
HOH
741
6
HOH
HOH
741
L
HOH
744
6
HOH
HOH
744
L
HOH
745
6
HOH
HOH
745
L
HOH
751
6
HOH
HOH
751
L
HOH
752
6
HOH
HOH
752
L
HOH
763
6
HOH
HOH
763
L
ILE
16
n
1
ILE
16
A
VAL
17
n
2
VAL
17
A
GLY
18
n
3
GLY
18
A
GLY
19
n
4
GLY
19
A
GLN
20
n
5
GLN
20
A
GLU
21
n
6
GLU
21
A
CYS
22
n
7
CYS
22
A
LYS
23
n
8
LYS
23
A
ASP
24
n
9
ASP
24
A
GLY
25
n
10
GLY
25
A
GLU
26
n
11
GLU
26
A
CYS
27
n
12
CYS
27
A
PRO
28
n
13
PRO
28
A
TRP
29
n
14
TRP
29
A
GLN
30
n
15
GLN
30
A
ALA
31
n
16
ALA
31
A
LEU
32
n
17
LEU
32
A
LEU
33
n
18
LEU
33
A
ILE
34
n
19
ILE
34
A
ASN
35
n
20
ASN
35
A
GLU
36
n
21
GLU
36
A
GLU
37
n
22
GLU
37
A
ASN
38
n
23
ASN
38
A
GLU
39
n
24
GLU
39
A
GLY
40
n
25
GLY
40
A
PHE
41
n
26
PHE
41
A
CYS
42
n
27
CYS
42
A
GLY
43
n
28
GLY
43
A
GLY
44
n
29
GLY
44
A
THR
45
n
30
THR
45
A
ILE
46
n
31
ILE
46
A
LEU
47
n
32
LEU
47
A
SER
48
n
33
SER
48
A
GLU
49
n
34
GLU
49
A
PHE
50
n
35
PHE
50
A
TYR
51
n
36
TYR
51
A
ILE
52
n
37
ILE
52
A
LEU
53
n
38
LEU
53
A
THR
54
n
39
THR
54
A
ALA
55
n
40
ALA
55
A
ALA
56
n
41
ALA
56
A
HIS
57
n
42
HIS
57
A
CYS
58
n
43
CYS
58
A
LEU
59
n
44
LEU
59
A
TYR
60
n
45
TYR
60
A
GLN
61
n
46
GLN
61
A
ALA
61
n
47
A
ALA
61
A
LYS
62
n
48
LYS
62
A
ARG
63
n
49
ARG
63
A
PHE
64
n
50
PHE
64
A
LYS
65
n
51
LYS
65
A
VAL
66
n
52
VAL
66
A
ARG
67
n
53
ARG
67
A
VAL
68
n
54
VAL
68
A
GLY
69
n
55
GLY
69
A
ASP
70
n
56
ASP
70
A
ARG
71
n
57
ARG
71
A
ASN
72
n
58
ASN
72
A
THR
73
n
59
THR
73
A
GLU
74
n
60
GLU
74
A
GLN
75
n
61
GLN
75
A
GLU
76
n
62
GLU
76
A
GLU
77
n
63
GLU
77
A
GLY
78
n
64
GLY
78
A
GLY
79
n
65
GLY
79
A
GLU
80
n
66
GLU
80
A
ALA
81
n
67
ALA
81
A
VAL
82
n
68
VAL
82
A
HIS
83
n
69
HIS
83
A
GLU
84
n
70
GLU
84
A
VAL
85
n
71
VAL
85
A
GLU
86
n
72
GLU
86
A
VAL
87
n
73
VAL
87
A
VAL
88
n
74
VAL
88
A
ILE
89
n
75
ILE
89
A
LYS
90
n
76
LYS
90
A
HIS
91
n
77
HIS
91
A
ASN
92
n
78
ASN
92
A
ARG
93
n
79
ARG
93
A
PHE
94
n
80
PHE
94
A
THR
95
n
81
THR
95
A
LYS
96
n
82
LYS
96
A
GLU
97
n
83
GLU
97
A
THR
98
n
84
THR
98
A
TYR
99
n
85
TYR
99
A
ASP
100
n
86
ASP
100
A
PHE
101
n
87
PHE
101
A
ASP
102
n
88
ASP
102
A
ILE
103
n
89
ILE
103
A
ALA
104
n
90
ALA
104
A
VAL
105
n
91
VAL
105
A
LEU
106
n
92
LEU
106
A
ARG
107
n
93
ARG
107
A
LEU
108
n
94
LEU
108
A
LYS
109
n
95
LYS
109
A
THR
110
n
96
THR
110
A
PRO
111
n
97
PRO
111
A
ILE
112
n
98
ILE
112
A
THR
113
n
99
THR
113
A
PHE
114
n
100
PHE
114
A
ARG
115
n
101
ARG
115
A
MET
116
n
102
MET
116
A
ASN
117
n
103
ASN
117
A
VAL
118
n
104
VAL
118
A
ALA
119
n
105
ALA
119
A
PRO
120
n
106
PRO
120
A
ALA
121
n
107
ALA
121
A
CYS
122
n
108
CYS
122
A
LEU
123
n
109
LEU
123
A
PRO
124
n
110
PRO
124
A
GLU
124
n
111
A
GLU
124
A
ARG
125
n
112
ARG
125
A
ASP
126
n
113
ASP
126
A
TRP
127
n
114
TRP
127
A
ALA
128
n
115
ALA
128
A
GLU
129
n
116
GLU
129
A
SER
130
n
117
SER
130
A
THR
131
n
118
THR
131
A
LEU
131
n
119
A
LEU
131
A
MET
131
n
120
B
MET
131
A
THR
132
n
121
THR
132
A
GLN
133
n
122
GLN
133
A
LYS
134
n
123
LYS
134
A
THR
135
n
124
THR
135
A
GLY
136
n
125
GLY
136
A
ILE
137
n
126
ILE
137
A
VAL
138
n
127
VAL
138
A
SER
139
n
128
SER
139
A
GLY
140
n
129
GLY
140
A
PHE
141
n
130
PHE
141
A
GLY
142
n
131
GLY
142
A
ARG
143
n
132
ARG
143
A
THR
144
n
133
THR
144
A
HIS
145
n
134
HIS
145
A
GLU
146
n
135
GLU
146
A
LYS
147
n
136
LYS
147
A
GLY
149
n
137
GLY
149
A
ARG
150
n
138
ARG
150
A
GLN
151
n
139
GLN
151
A
SER
152
n
140
SER
152
A
THR
153
n
141
THR
153
A
ARG
154
n
142
ARG
154
A
LEU
155
n
143
LEU
155
A
LYS
156
n
144
LYS
156
A
MET
157
n
145
MET
157
A
LEU
158
n
146
LEU
158
A
GLU
159
n
147
GLU
159
A
VAL
160
n
148
VAL
160
A
PRO
161
n
149
PRO
161
A
TYR
162
n
150
TYR
162
A
VAL
163
n
151
VAL
163
A
ASP
164
n
152
ASP
164
A
ARG
165
n
153
ARG
165
A
ASN
166
n
154
ASN
166
A
SER
167
n
155
SER
167
A
CYS
168
n
156
CYS
168
A
LYS
169
n
157
LYS
169
A
LEU
170
n
158
LEU
170
A
SER
171
n
159
SER
171
A
SER
172
n
160
SER
172
A
SER
173
n
161
SER
173
A
PHE
174
n
162
PHE
174
A
ILE
175
n
163
ILE
175
A
ILE
176
n
164
ILE
176
A
THR
177
n
165
THR
177
A
GLN
178
n
166
GLN
178
A
ASN
179
n
167
ASN
179
A
MET
180
n
168
MET
180
A
PHE
181
n
169
PHE
181
A
CYS
182
n
170
CYS
182
A
ALA
183
n
171
ALA
183
A
GLY
184
n
172
GLY
184
A
TYR
185
n
173
TYR
185
A
ASP
185
n
174
A
ASP
185
A
THR
185
n
175
B
THR
185
A
LYS
186
n
176
LYS
186
A
GLN
187
n
177
GLN
187
A
GLU
188
n
178
GLU
188
A
ASP
189
n
179
ASP
189
A
ALA
190
n
180
ALA
190
A
CYS
191
n
181
CYS
191
A
GLN
192
n
182
GLN
192
A
GLY
193
n
183
GLY
193
A
ASP
194
n
184
ASP
194
A
SER
195
n
185
SER
195
A
GLY
196
n
186
GLY
196
A
GLY
197
n
187
GLY
197
A
PRO
198
n
188
PRO
198
A
HIS
199
n
189
HIS
199
A
VAL
200
n
190
VAL
200
A
THR
201
n
191
THR
201
A
ARG
202
n
192
ARG
202
A
PHE
203
n
193
PHE
203
A
LYS
204
n
194
LYS
204
A
ASP
205
n
195
ASP
205
A
THR
206
n
196
THR
206
A
TYR
207
n
197
TYR
207
A
PHE
208
n
198
PHE
208
A
VAL
209
n
199
VAL
209
A
THR
210
n
200
THR
210
A
GLY
211
n
201
GLY
211
A
ILE
212
n
202
ILE
212
A
VAL
213
n
203
VAL
213
A
SER
214
n
204
SER
214
A
TRP
215
n
205
TRP
215
A
GLY
216
n
206
GLY
216
A
GLU
217
n
207
GLU
217
A
GLY
218
n
208
GLY
218
A
CYS
220
n
209
CYS
220
A
ALA
221
n
210
ALA
221
A
ARG
222
n
211
ARG
222
A
LYS
223
n
212
LYS
223
A
GLY
223
n
213
A
GLY
223
A
LYS
224
n
214
LYS
224
A
TYR
225
n
215
TYR
225
A
GLY
226
n
216
GLY
226
A
ILE
227
n
217
ILE
227
A
TYR
228
n
218
TYR
228
A
THR
229
n
219
THR
229
A
LYS
230
n
220
LYS
230
A
VAL
231
n
221
VAL
231
A
THR
232
n
222
THR
232
A
ALA
233
n
223
ALA
233
A
PHE
234
n
224
PHE
234
A
LEU
235
n
225
LEU
235
A
LYS
236
n
226
LYS
236
A
TRP
237
n
227
TRP
237
A
ILE
238
n
228
ILE
238
A
ASP
239
n
229
ASP
239
A
ARG
240
n
230
ARG
240
A
SER
241
n
231
SER
241
A
MET
242
n
232
MET
242
A
LYS
243
n
233
LYS
243
A
LYS
87
n
1
LYS
87
L
LEU
88
n
2
LEU
88
L
CYS
89
n
3
CYS
89
L
SER
90
n
4
SER
90
L
LEU
91
n
5
LEU
91
L
ASP
92
n
6
ASP
92
L
ASN
93
n
7
ASN
93
L
GLY
94
n
8
GLY
94
L
ASP
95
n
9
ASP
95
L
CYS
96
n
10
CYS
96
L
ASP
97
n
11
ASP
97
L
GLN
98
n
12
GLN
98
L
PHE
99
n
13
PHE
99
L
CYS
100
n
14
CYS
100
L
HIS
101
n
15
HIS
101
L
GLU
102
n
16
GLU
102
L
GLU
103
n
17
GLU
103
L
GLN
104
n
18
GLN
104
L
ASN
105
n
19
ASN
105
L
SER
106
n
20
SER
106
L
VAL
107
n
21
VAL
107
L
VAL
108
n
22
VAL
108
L
CYS
109
n
23
CYS
109
L
SER
110
n
24
SER
110
L
CYS
111
n
25
CYS
111
L
ALA
112
n
26
ALA
112
L
ARG
113
n
27
ARG
113
L
GLY
114
n
28
GLY
114
L
TYR
115
n
29
TYR
115
L
THR
116
n
30
THR
116
L
LEU
117
n
31
LEU
117
L
ALA
118
n
32
ALA
118
L
ASP
119
n
33
ASP
119
L
ASN
120
n
34
ASN
120
L
GLY
121
n
35
GLY
121
L
LYS
122
n
36
LYS
122
L
ALA
123
n
37
ALA
123
L
CYS
124
n
38
CYS
124
L
ILE
125
n
39
ILE
125
L
PRO
126
n
40
PRO
126
L
THR
127
n
41
THR
127
L
GLY
128
n
42
GLY
128
L
PRO
129
n
43
PRO
129
L
TYR
130
n
44
TYR
130
L
PRO
131
n
45
PRO
131
L
CYS
132
n
46
CYS
132
L
GLY
133
n
47
GLY
133
L
LYS
134
n
48
LYS
134
L
GLN
135
n
49
GLN
135
L
THR
136
n
50
THR
136
L
LEU
137
n
51
LEU
137
L
author_and_software_defined_assembly
PISA
2
dimeric
3630
-43
12690
A
ASP
70
A
OD2
ASP
56
1_555
A
CA
501
C
CA
CA
1_555
A
ASN
72
A
O
ASN
58
1_555
83.7
A
ASP
70
A
OD2
ASP
56
1_555
A
CA
501
C
CA
CA
1_555
A
GLU
77
A
OE2
GLU
63
1_555
78.7
A
ASN
72
A
O
ASN
58
1_555
A
CA
501
C
CA
CA
1_555
A
GLU
77
A
OE2
GLU
63
1_555
83.4
A
ASP
70
A
OD2
ASP
56
1_555
A
CA
501
C
CA
CA
1_555
A
HOH
710
H
O
HOH
1_555
77.0
A
ASN
72
A
O
ASN
58
1_555
A
CA
501
C
CA
CA
1_555
A
HOH
710
H
O
HOH
1_555
96.1
A
GLU
77
A
OE2
GLU
63
1_555
A
CA
501
C
CA
CA
1_555
A
HOH
710
H
O
HOH
1_555
155.6
A
ASP
70
A
OD2
ASP
56
1_555
A
CA
501
C
CA
CA
1_555
A
GLN
75
A
O
GLN
61
1_555
168.9
A
ASN
72
A
O
ASN
58
1_555
A
CA
501
C
CA
CA
1_555
A
GLN
75
A
O
GLN
61
1_555
105.4
A
GLU
77
A
OE2
GLU
63
1_555
A
CA
501
C
CA
CA
1_555
A
GLN
75
A
O
GLN
61
1_555
95.8
A
HOH
710
H
O
HOH
1_555
A
CA
501
C
CA
CA
1_555
A
GLN
75
A
O
GLN
61
1_555
107.8
A
ASP
70
A
OD2
ASP
56
1_555
A
CA
501
C
CA
CA
1_555
A
GLU
80
A
OE2
GLU
66
1_555
85.3
A
ASN
72
A
O
ASN
58
1_555
A
CA
501
C
CA
CA
1_555
A
GLU
80
A
OE2
GLU
66
1_555
168.2
A
GLU
77
A
OE2
GLU
63
1_555
A
CA
501
C
CA
CA
1_555
A
GLU
80
A
OE2
GLU
66
1_555
90.2
A
HOH
710
H
O
HOH
1_555
A
CA
501
C
CA
CA
1_555
A
GLU
80
A
OE2
GLU
66
1_555
85.6
A
GLN
75
A
O
GLN
61
1_555
A
CA
501
C
CA
CA
1_555
A
GLU
80
A
OE2
GLU
66
1_555
85.0
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
GLN
20
A
N
GLN
5
A
O
MET
157
A
O
MET
145
A
O
VAL
160
A
O
VAL
148
A
N
GLY
136
A
N
GLY
125
A
N
ILE
137
A
N
ILE
126
A
O
VAL
200
A
O
VAL
190
A
N
PHE
203
A
N
PHE
193
A
O
THR
206
A
O
THR
196
A
N
TRP
215
A
N
TRP
205
A
O
ILE
227
A
O
ILE
217
A
O
TYR
228
A
O
TYR
218
A
N
PHE
181
A
N
PHE
169
A
N
LEU
33
A
N
LEU
18
A
O
PHE
41
A
O
PHE
26
A
N
THR
45
A
N
THR
30
A
O
LEU
53
A
O
LEU
38
A
N
THR
54
A
N
THR
39
A
O
ALA
104
A
O
ALA
90
A
O
VAL
105
A
O
VAL
91
A
N
ILE
89
A
N
ILE
75
A
O
HIS
83
A
O
HIS
69
A
N
VAL
66
A
N
VAL
52
A
O
ARG
67
A
O
ARG
53
A
N
LEU
32
A
N
LEU
17
L
N
HIS
101
B
N
HIS
15
L
O
VAL
108
B
O
VAL
22
L
N
THR
116
B
N
THR
30
L
O
ILE
125
B
O
ILE
39
1
A
GLU
74
-115.08
65.36
1
A
GLN
75
174.39
129.53
1
A
ARG
115
-174.96
-177.31
1
A
ALA
221
59.30
14.95
1
L
LEU
88
48.93
-116.12
1
L
ASN
93
48.46
23.40
1
L
GLN
98
-119.81
-114.23
PARHCSDX.PRO,PARAM11.WAT
TOPHCSDX.PRO
36.34
-2.94990
0.00000
0.00000
8.68510
0.00000
-5.73510
FINAL REFINEMENT HAD A B FACTOR OPTIMIZATION AND A FINAL POWELL MINIMIZATION.
0.268
0.186
0.19
2.10
8.00
643
19603
17183
4.000
99.1
RANDOM
1
Isotropic
2.0
0.0
DIRECT REPLACEMENT
PDB ENTRY 1FJS
Engh & Huber
2.10
8.00
164
2439
55
0
2220
0.011
2.01
1.59
1.500
2.000
2.000
2.500
0.3366
0.2932
2.19
55
1276
1276
8
4.10
0.2688
0.2802
2.31
60
1503
8
0.2872
0.262
2.45
73
1683
8
0.2919
0.2416
2.63
74
1759
8
0.3213
0.2235
2.88
72
1944
8
0.2466
0.1949
3.28
89
2081
8
0.2824
0.1512
4.04
109
2249
8
0.2374
0.1474
8.0
111
2383
8
56.09
2.100
25.00
1MQ6
19603
19603
0.0
-3.0
0.0673
1
8.5000
3.540
99.1
2.10
2.23
1.30
3162
0.3613
1
3.50
98.4
data collection
Blu-Ice
data reduction
X-GEN
model building
X-PLOR
refinement
X-PLOR
3.1
data scaling
X-GEN
phasing
X-PLOR
COAGULATION FACTOR X (E.C.3.4.21.6)
Crystal Structure of 3-chloro-N-[4-chloro-2-[[(5-chloro-2-pyridinyl)amino]carbonyl]-6-methoxyphenyl]-4-[[(4,5-dihydro-2-oxazolyl)methylamino]methyl]-2-thiophenecarboxamide Complexed with Human Factor Xa
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
N
N
6
N
N
6
N
N
Factor Xa forms a complex with factor Va in the presence of calcium and a phospholipid membrane to produce the prothrombinase complex.
A
ALA
55
A
ALA
40
HELX_P
A
GLN
61
A
GLN
46
5
1
7
A
GLU
124
A
GLU
111
HELX_P
A
THR
131
A
THR
118
1
2
8
A
A
LEU
131
A
LEU
119
HELX_P
A
GLN
133
A
GLN
122
5
3
4
A
A
ASP
164
A
ASP
152
HELX_P
A
SER
172
A
SER
160
1
4
9
A
PHE
234
A
PHE
224
HELX_P
A
MET
242
A
MET
232
1
5
9
L
LYS
87
B
LYS
1
HELX_P
L
CYS
96
B
CYS
10
5
6
10
disulf
2.040
A
CYS
22
A
SG
CYS
7
1_555
A
CYS
27
A
SG
CYS
12
1_555
disulf
2.046
A
CYS
42
A
SG
CYS
27
1_555
A
CYS
58
A
SG
CYS
43
1_555
disulf
2.056
A
CYS
122
A
SG
CYS
108
1_555
L
CYS
132
B
SG
CYS
46
1_555
disulf
2.008
A
CYS
168
A
SG
CYS
156
1_555
A
CYS
182
A
SG
CYS
170
1_555
disulf
2.018
A
CYS
191
A
SG
CYS
181
1_555
A
CYS
220
A
SG
CYS
209
1_555
disulf
2.058
L
CYS
89
B
SG
CYS
3
1_555
L
CYS
100
B
SG
CYS
14
1_555
disulf
2.012
L
CYS
96
B
SG
CYS
10
1_555
L
CYS
109
B
SG
CYS
23
1_555
disulf
2.040
L
CYS
111
B
SG
CYS
25
1_555
L
CYS
124
B
SG
CYS
38
1_555
metalc
2.397
A
CA
501
C
CA
CA
1_555
A
ASP
70
A
OD2
ASP
56
1_555
metalc
2.095
A
CA
501
C
CA
CA
1_555
A
ASN
72
A
O
ASN
58
1_555
metalc
2.103
A
CA
501
C
CA
CA
1_555
A
GLU
77
A
OE2
GLU
63
1_555
metalc
1.810
A
CA
501
C
CA
CA
1_555
A
HOH
710
H
O
HOH
1_555
metalc
1.990
A
CA
501
C
CA
CA
1_555
A
GLN
75
A
O
GLN
61
1_555
metalc
2.088
A
CA
501
C
CA
CA
1_555
A
GLU
80
A
OE2
GLU
66
1_555
BLOOD CLOTTING
PROTEIN INHIBITOR COMPLEX, COAGULATION COFACTOR, PROTEASE, BLOOD CLOTTING
FA10_HUMAN
UNP
1
235
P00742
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRF
TKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSS
SFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMK
FA10_HUMAN
UNP
2
127
P00742
KLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTL
235
467
1MQ6
16
243
P00742
A
1
1
233
127
177
1MQ6
87
137
P00742
L
2
1
51
7
7
2
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLN
20
A
GLN
5
A
GLU
21
A
GLU
6
A
LYS
156
A
LYS
144
A
PRO
161
A
PRO
149
A
THR
135
A
THR
124
A
GLY
140
A
GLY
129
A
PRO
198
A
PRO
188
A
PHE
203
A
PHE
193
A
THR
206
A
THR
196
A
TRP
215
A
TRP
205
A
GLY
226
A
GLY
216
A
LYS
230
A
LYS
220
A
MET
180
A
MET
168
A
ALA
183
A
ALA
171
A
GLN
30
A
GLN
15
A
ASN
35
A
ASN
20
A
GLY
40
A
GLY
25
A
ILE
46
A
ILE
31
A
TYR
51
A
TYR
36
A
THR
54
A
THR
39
A
ALA
104
A
ALA
90
A
LEU
108
A
LEU
94
A
ALA
81
A
ALA
67
A
LYS
90
A
LYS
76
A
PHE
64
A
PHE
50
A
VAL
68
A
VAL
54
A
GLN
30
A
GLN
15
A
ASN
35
A
ASN
20
L
PHE
99
B
PHE
13
L
GLU
102
B
GLU
16
L
VAL
107
B
VAL
21
L
SER
110
B
SER
24
L
TYR
115
B
TYR
29
L
LEU
117
B
LEU
31
L
CYS
124
B
CYS
38
L
PRO
126
B
PRO
40
BINDING SITE FOR RESIDUE CA A 501
Software
6
BINDING SITE FOR RESIDUE XLD A 500
Software
17
BINDING SITE FOR RESIDUE GOL A 502
Software
7
BINDING SITE FOR RESIDUE GOL A 503
Software
4
BINDING SITE FOR RESIDUE GOL A 504
Software
3
A
ASP
70
A
ASP
56
6
1_555
A
ASN
72
A
ASN
58
6
1_555
A
GLN
75
A
GLN
61
6
1_555
A
GLU
77
A
GLU
63
6
1_555
A
GLU
80
A
GLU
66
6
1_555
A
HOH
710
H
HOH
6
1_555
A
LYS
96
A
LYS
82
17
1_555
A
GLU
97
A
GLU
83
17
1_555
A
TYR
99
A
TYR
85
17
1_555
A
GLU
146
A
GLU
135
17
1_555
A
PHE
174
A
PHE
162
17
1_555
A
ASP
189
A
ASP
179
17
1_555
A
ALA
190
A
ALA
180
17
1_555
A
GLN
192
A
GLN
182
17
1_555
A
VAL
213
A
VAL
203
17
1_555
A
TRP
215
A
TRP
205
17
1_555
A
GLY
216
A
GLY
206
17
1_555
A
GLU
217
A
GLU
207
17
1_555
A
GLY
218
A
GLY
208
17
1_555
A
CYS
220
A
CYS
209
17
1_555
A
GLY
226
A
GLY
216
17
1_555
A
TYR
228
A
TYR
218
17
1_555
A
HOH
736
H
HOH
17
1_555
A
LEU
47
A
LEU
32
7
1_555
A
SER
48
A
SER
33
7
1_555
A
GLU
49
A
GLU
34
7
1_555
A
PHE
114
A
PHE
100
7
1_555
A
PRO
120
A
PRO
106
7
1_555
A
HOH
702
H
HOH
7
1_555
L
TYR
130
B
TYR
44
7
1_555
A
LEU
123
A
LEU
109
4
1_555
A
PRO
124
A
PRO
110
4
1_555
A
LEU
235
A
LEU
225
4
1_555
A
HOH
672
H
HOH
4
1_555
A
GLU
84
A
GLU
70
3
3_645
A
SER
130
A
SER
117
3
1_555
L
CYS
100
B
CYS
14
3
1_555
19
P 21 21 21