0.015924
0.009193
0.000000
0.000000
0.018387
0.000000
0.000000
0.000000
0.011976
0.00000
0.00000
0.00000
GLY B 49 - ILE B 50 OMEGA = 147.56 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
THERE ARE HYDROXYL GROUPS COVALENTLY BOUND TO SG CYS A 67 AND SG CYS B 67. THEY ARE PRESENTED ON HETATM RECORDS FOLLOWING THE END OF EACH CHAIN.
Chang, C.-H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
62.800
62.800
83.500
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
C3 H7 N O3 S
137.158
n
S-HYDROXYCYSTEINE
L-peptide linking
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
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
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
C41 H38 N2 O3
606.752
[4R-(4ALPHA,5ALPHA,6BETA,7BETA)]-HEXAHYDRO-5,6-DIHYDROXY-1,3-BIS[2-NAPHTHYL-METHYL]-4,7-BIS(PHENYLMETHYL)-2H-1,3-DIAZEPIN-2-ONE
non-polymer
US
Science
SCIEAS
0038
0036-8075
263
380
384
8278812
Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors.
1994
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
x-ray
1
1.0
10773.664
HIV-1 PROTEASE
2
man
polymer
606.752
[4R-(4ALPHA,5ALPHA,6BETA,7BETA)]-HEXAHYDRO-5,6-DIHYDROXY-1,3-BIS[2-NAPHTHYL-METHYL]-4,7-BIS(PHENYLMETHYL)-2H-1,3-DIAZEPIN-2-ONE
1
syn
non-polymer
no
yes
PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEI(CSO)GHKAIGTVL
VGPTPVNIIGRNLLTQIGATLNF
PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGATLNF
A,B
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
Lentivirus
Escherichia
sample
11676
Human immunodeficiency virus 1
562
Escherichia coli
2.21
44.29
pdbx_database_status
struct_conf
struct_conf_type
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1995-01-26
1
1
2008-03-03
1
2
2011-07-13
1
3
2012-02-29
1
4
2017-11-29
_pdbx_database_status.process_site
Y
BNL
1994-02-14
REL
XK2
[4R-(4ALPHA,5ALPHA,6BETA,7BETA)]-HEXAHYDRO-5,6-DIHYDROXY-1,3-BIS[2-NAPHTHYL-METHYL]-4,7-BIS(PHENYLMETHYL)-2H-1,3-DIAZEPIN-2-ONE
XK2
263
2
XK2
XK2
263
A
PRO
1
n
1
PRO
1
A
GLN
2
n
2
GLN
2
A
VAL
3
n
3
VAL
3
A
THR
4
n
4
THR
4
A
LEU
5
n
5
LEU
5
A
TRP
6
n
6
TRP
6
A
GLN
7
n
7
GLN
7
A
ARG
8
n
8
ARG
8
A
PRO
9
n
9
PRO
9
A
LEU
10
n
10
LEU
10
A
VAL
11
n
11
VAL
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
LYS
14
n
14
LYS
14
A
ILE
15
n
15
ILE
15
A
GLY
16
n
16
GLY
16
A
GLY
17
n
17
GLY
17
A
GLN
18
n
18
GLN
18
A
LEU
19
n
19
LEU
19
A
LYS
20
n
20
LYS
20
A
GLU
21
n
21
GLU
21
A
ALA
22
n
22
ALA
22
A
LEU
23
n
23
LEU
23
A
LEU
24
n
24
LEU
24
A
ASP
25
n
25
ASP
25
A
THR
26
n
26
THR
26
A
GLY
27
n
27
GLY
27
A
ALA
28
n
28
ALA
28
A
ASP
29
n
29
ASP
29
A
ASP
30
n
30
ASP
30
A
THR
31
n
31
THR
31
A
VAL
32
n
32
VAL
32
A
LEU
33
n
33
LEU
33
A
GLU
34
n
34
GLU
34
A
GLU
35
n
35
GLU
35
A
MET
36
n
36
MET
36
A
SER
37
n
37
SER
37
A
LEU
38
n
38
LEU
38
A
PRO
39
n
39
PRO
39
A
GLY
40
n
40
GLY
40
A
ARG
41
n
41
ARG
41
A
TRP
42
n
42
TRP
42
A
LYS
43
n
43
LYS
43
A
PRO
44
n
44
PRO
44
A
LYS
45
n
45
LYS
45
A
MET
46
n
46
MET
46
A
ILE
47
n
47
ILE
47
A
GLY
48
n
48
GLY
48
A
GLY
49
n
49
GLY
49
A
ILE
50
n
50
ILE
50
A
GLY
51
n
51
GLY
51
A
GLY
52
n
52
GLY
52
A
PHE
53
n
53
PHE
53
A
ILE
54
n
54
ILE
54
A
LYS
55
n
55
LYS
55
A
VAL
56
n
56
VAL
56
A
ARG
57
n
57
ARG
57
A
GLN
58
n
58
GLN
58
A
TYR
59
n
59
TYR
59
A
ASP
60
n
60
ASP
60
A
GLN
61
n
61
GLN
61
A
ILE
62
n
62
ILE
62
A
LEU
63
n
63
LEU
63
A
ILE
64
n
64
ILE
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
CSO
67
n
67
CSO
67
A
GLY
68
n
68
GLY
68
A
HIS
69
n
69
HIS
69
A
LYS
70
n
70
LYS
70
A
ALA
71
n
71
ALA
71
A
ILE
72
n
72
ILE
72
A
GLY
73
n
73
GLY
73
A
THR
74
n
74
THR
74
A
VAL
75
n
75
VAL
75
A
LEU
76
n
76
LEU
76
A
VAL
77
n
77
VAL
77
A
GLY
78
n
78
GLY
78
A
PRO
79
n
79
PRO
79
A
THR
80
n
80
THR
80
A
PRO
81
n
81
PRO
81
A
VAL
82
n
82
VAL
82
A
ASN
83
n
83
ASN
83
A
ILE
84
n
84
ILE
84
A
ILE
85
n
85
ILE
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
ASN
88
n
88
ASN
88
A
LEU
89
n
89
LEU
89
A
LEU
90
n
90
LEU
90
A
THR
91
n
91
THR
91
A
GLN
92
n
92
GLN
92
A
ILE
93
n
93
ILE
93
A
GLY
94
n
94
GLY
94
A
ALA
95
n
95
ALA
95
A
THR
96
n
96
THR
96
A
LEU
97
n
97
LEU
97
A
ASN
98
n
98
ASN
98
A
PHE
99
n
99
PHE
99
A
PRO
1
n
1
PRO
1
B
GLN
2
n
2
GLN
2
B
VAL
3
n
3
VAL
3
B
THR
4
n
4
THR
4
B
LEU
5
n
5
LEU
5
B
TRP
6
n
6
TRP
6
B
GLN
7
n
7
GLN
7
B
ARG
8
n
8
ARG
8
B
PRO
9
n
9
PRO
9
B
LEU
10
n
10
LEU
10
B
VAL
11
n
11
VAL
11
B
THR
12
n
12
THR
12
B
ILE
13
n
13
ILE
13
B
LYS
14
n
14
LYS
14
B
ILE
15
n
15
ILE
15
B
GLY
16
n
16
GLY
16
B
GLY
17
n
17
GLY
17
B
GLN
18
n
18
GLN
18
B
LEU
19
n
19
LEU
19
B
LYS
20
n
20
LYS
20
B
GLU
21
n
21
GLU
21
B
ALA
22
n
22
ALA
22
B
LEU
23
n
23
LEU
23
B
LEU
24
n
24
LEU
24
B
ASP
25
n
25
ASP
25
B
THR
26
n
26
THR
26
B
GLY
27
n
27
GLY
27
B
ALA
28
n
28
ALA
28
B
ASP
29
n
29
ASP
29
B
ASP
30
n
30
ASP
30
B
THR
31
n
31
THR
31
B
VAL
32
n
32
VAL
32
B
LEU
33
n
33
LEU
33
B
GLU
34
n
34
GLU
34
B
GLU
35
n
35
GLU
35
B
MET
36
n
36
MET
36
B
SER
37
n
37
SER
37
B
LEU
38
n
38
LEU
38
B
PRO
39
n
39
PRO
39
B
GLY
40
n
40
GLY
40
B
ARG
41
n
41
ARG
41
B
TRP
42
n
42
TRP
42
B
LYS
43
n
43
LYS
43
B
PRO
44
n
44
PRO
44
B
LYS
45
n
45
LYS
45
B
MET
46
n
46
MET
46
B
ILE
47
n
47
ILE
47
B
GLY
48
n
48
GLY
48
B
GLY
49
n
49
GLY
49
B
ILE
50
n
50
ILE
50
B
GLY
51
n
51
GLY
51
B
GLY
52
n
52
GLY
52
B
PHE
53
n
53
PHE
53
B
ILE
54
n
54
ILE
54
B
LYS
55
n
55
LYS
55
B
VAL
56
n
56
VAL
56
B
ARG
57
n
57
ARG
57
B
GLN
58
n
58
GLN
58
B
TYR
59
n
59
TYR
59
B
ASP
60
n
60
ASP
60
B
GLN
61
n
61
GLN
61
B
ILE
62
n
62
ILE
62
B
LEU
63
n
63
LEU
63
B
ILE
64
n
64
ILE
64
B
GLU
65
n
65
GLU
65
B
ILE
66
n
66
ILE
66
B
CSO
67
n
67
CSO
67
B
GLY
68
n
68
GLY
68
B
HIS
69
n
69
HIS
69
B
LYS
70
n
70
LYS
70
B
ALA
71
n
71
ALA
71
B
ILE
72
n
72
ILE
72
B
GLY
73
n
73
GLY
73
B
THR
74
n
74
THR
74
B
VAL
75
n
75
VAL
75
B
LEU
76
n
76
LEU
76
B
VAL
77
n
77
VAL
77
B
GLY
78
n
78
GLY
78
B
PRO
79
n
79
PRO
79
B
THR
80
n
80
THR
80
B
PRO
81
n
81
PRO
81
B
VAL
82
n
82
VAL
82
B
ASN
83
n
83
ASN
83
B
ILE
84
n
84
ILE
84
B
ILE
85
n
85
ILE
85
B
GLY
86
n
86
GLY
86
B
ARG
87
n
87
ARG
87
B
ASN
88
n
88
ASN
88
B
LEU
89
n
89
LEU
89
B
LEU
90
n
90
LEU
90
B
THR
91
n
91
THR
91
B
GLN
92
n
92
GLN
92
B
ILE
93
n
93
ILE
93
B
GLY
94
n
94
GLY
94
B
ALA
95
n
95
ALA
95
B
THR
96
n
96
THR
96
B
LEU
97
n
97
LEU
97
B
ASN
98
n
98
ASN
98
B
PHE
99
n
99
PHE
99
B
author_and_software_defined_assembly
PISA
2
dimeric
5250
-35
9040
A
CSO
67
S-HYDROXYCYSTEINE
A
CSO
67
CYS
B
CSO
67
S-HYDROXYCYSTEINE
B
CSO
67
CYS
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
1
B
B
GLY
ILE
49
50
147.56
1
-13.16
2.00
111.60
98.44
A
A
A
CB
CA
C
ILE
ILE
ILE
15
15
15
N
1
4.70
0.50
120.30
125.00
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
87
87
87
N
1
A
A
CE2
CD2
TRP
TRP
6
6
0.078
0.012
1.409
1.487
N
1
A
A
CE2
CD2
TRP
TRP
42
42
0.093
0.012
1.409
1.502
N
1
B
B
CE2
CD2
TRP
TRP
6
6
0.081
0.012
1.409
1.490
N
1
B
B
CE2
CD2
TRP
TRP
42
42
0.087
0.012
1.409
1.496
N
1
A
GLU
35
-38.63
118.80
1
A
PRO
39
-53.44
99.94
1
A
CSO
67
47.09
-153.40
0.1930000
0.1930000
1.8
12695
1
2.
1.8
0
1560
46
0
1514
0.016
3.3
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) PROTEASE COMPLEXED WITH XK263 OF DUPONT MERCK
RATIONAL DESIGN OF POTENT, BIOAVAILABLE, NONPEPTIDE CYCLIC UREAS AS HIV PROTEASE INHIBITORS
1
N
N
1
N
N
2
N
N
A
GLY
86
A
GLY
86
HELX_P
A
GLY
94
A
GLY
94
1
HA
9
B
GLY
86
B
GLY
86
HELX_P
B
GLY
94
B
GLY
94
1
HB
9
covale
1.332
A
ILE
66
A
C
ILE
66
1_555
A
CSO
67
A
N
CSO
67
1_555
covale
1.335
A
CSO
67
A
C
CSO
67
1_555
A
GLY
68
A
N
GLY
68
1_555
covale
1.303
B
ILE
66
B
C
ILE
66
1_555
B
CSO
67
B
N
CSO
67
1_555
covale
1.333
B
CSO
67
B
C
CSO
67
1_555
B
GLY
68
B
N
GLY
68
1_555
HYDROLASE/HYDROLASE INHIBITOR
HYDROLASE, ACID PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR complex
POL_HV1H2
UNP
1
1
P04585
FFREDLAFLQGKAREFSSEQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQVTLWQRPLVTIKIGGQLKEALL
DTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPISPI
ETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQ
DFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMT
KILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIV
LPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDL
IAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEY
WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLDGI
DKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIE
AEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQV
RDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRNPLWKGPAKLLWKG
EGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED
57
155
1HVR
1
99
P04585
A
1
1
99
57
155
1HVR
1
99
P04585
B
1
1
99
1
CYS
CONFLICT
ALA
95
1HVR
A
P04585
UNP
151
95
2
CYS
CONFLICT
ALA
95
1HVR
B
P04585
UNP
151
95
8
8
4
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
HIS
69
A
HIS
69
A
GLY
78
A
GLY
78
A
THR
31
A
THR
31
A
GLU
34
A
GLU
34
A
ASN
83
A
ASN
83
A
ILE
85
A
ILE
85
A
GLN
18
A
GLN
18
A
ASP
25
A
ASP
25
A
PRO
9
A
PRO
9
A
ILE
15
A
ILE
15
A
GLU
65
A
GLU
65
A
ILE
66
A
ILE
66
B
LYS
43
B
LYS
43
B
GLY
49
B
GLY
49
B
GLY
52
B
GLY
52
B
ILE
66
B
ILE
66
B
HIS
69
B
HIS
69
B
GLY
78
B
GLY
78
B
THR
31
B
THR
31
B
GLU
34
B
GLU
34
B
ASN
83
B
ASN
83
B
ILE
85
B
ILE
85
B
GLN
18
B
GLN
18
B
ASP
25
B
ASP
25
B
PRO
9
B
PRO
9
B
ILE
15
B
ILE
15
B
GLU
65
B
GLU
65
B
ILE
66
B
ILE
66
A
PRO
1
A
PRO
1
A
THR
4
A
THR
4
B
THR
96
B
THR
96
B
PHE
99
B
PHE
99
A
THR
96
A
THR
96
A
PHE
99
A
PHE
99
B
PRO
1
B
PRO
1
B
THR
4
B
THR
4
BINDING SITE FOR RESIDUE XK2 A 263
Software
18
A
ARG
8
A
ARG
8
18
1_555
A
ASP
25
A
ASP
25
18
1_555
A
GLY
27
A
GLY
27
18
1_555
A
ALA
28
A
ALA
28
18
1_555
A
ASP
30
A
ASP
30
18
1_555
A
GLY
48
A
GLY
48
18
1_555
A
GLY
49
A
GLY
49
18
1_555
A
ILE
50
A
ILE
50
18
1_555
A
ILE
84
A
ILE
84
18
1_555
B
ASP
25
B
ASP
25
18
1_555
B
GLY
27
B
GLY
27
18
1_555
B
ALA
28
B
ALA
28
18
1_555
B
ASP
30
B
ASP
30
18
1_555
B
VAL
32
B
VAL
32
18
1_555
B
GLY
48
B
GLY
48
18
1_555
B
GLY
49
B
GLY
49
18
1_555
B
ILE
50
B
ILE
50
18
1_555
B
PRO
81
B
PRO
81
18
1_555
169
P 61