0.015898
0.009179
0.000000
0.000000
0.018358
0.000000
0.000000
0.000000
0.011976
0.00000
0.00000
0.00000
Chang, C.-H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
62.900
62.900
83.500
C25 H30 N2 O3
406.517
[4-R-(4-ALPHA,6-BETA,7-BETA]-HEXAHYDRO-5,6-DI(HYDROXY)-1,3-DI(ALLYL)-4,7-BISPHENYLMETHYL)-2H-1,3-DIAZEPINONE
XK216
non-polymer
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 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
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
273
12325
12331
10.1074/jbc.273.20.12325
9575185
Molecular recognition of cyclic urea HIV-1 protease inhibitors.
1998
10.2210/pdb1hwr/pdb
pdb_00001hwr
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
10757.664
HIV-1 PROTEASE
3.4.23.16
2
man
polymer
406.517
[4-R-(4-ALPHA,6-BETA,7-BETA]-HEXAHYDRO-5,6-DI(HYDROXY)-1,3-DI(ALLYL)-4,7-BISPHENYLMETHYL)-2H-1,3-DIAZEPINONE
1
syn
non-polymer
no
no
PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGATLNF
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
BH102
Escherichia
sample
11676
Human immunodeficiency virus 1
562
Escherichia coli
2.22
45.0
pdbx_database_status
struct_conf
struct_conf_type
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Derived calculations
Other
Database references
Derived calculations
Refinement description
1
0
1999-03-23
1
1
2008-03-03
1
2
2011-07-13
1
3
2017-11-29
1
4
2023-08-09
_pdbx_database_status.process_site
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1998-03-20
REL
216
[4-R-(4-ALPHA,6-BETA,7-BETA]-HEXAHYDRO-5,6-DI(HYDROXY)-1,3-DI(ALLYL)-4,7-BISPHENYLMETHYL)-2H-1,3-DIAZEPINONE
1HVR
PDB
experimental model
216
216
2
216
216
216
B
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
CYS
67
n
67
CYS
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
CYS
67
n
67
CYS
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
4640
-31
9190
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
O
GLN
18
A
O
GLN
18
A
N
ILE
15
A
N
ILE
15
A
O
LYS
14
A
O
LYS
14
A
N
GLU
65
A
N
GLU
65
A
O
ILE
62
A
O
ILE
62
A
N
GLY
73
A
N
GLY
73
A
O
LYS
43
A
O
LYS
43
A
N
GLN
58
A
N
GLN
58
A
O
ARG
57
A
O
ARG
57
A
N
VAL
77
A
N
VAL
77
B
O
GLN
18
B
O
GLN
18
B
N
ILE
15
B
N
ILE
15
B
O
LYS
14
B
O
LYS
14
B
N
GLU
65
B
N
GLU
65
B
O
ILE
62
B
O
ILE
62
B
N
GLY
73
B
N
GLY
73
B
O
LEU
33
B
O
LEU
33
B
N
LEU
76
B
N
LEU
76
B
O
VAL
75
B
O
VAL
75
B
N
TYR
59
B
N
TYR
59
B
O
ILE
54
B
O
ILE
54
B
N
ILE
47
B
N
ILE
47
1
A
A
ILE
CYS
66
67
-145.35
1
A
ARG
8
0.097
SIDE CHAIN
1
A
ARG
57
0.097
SIDE CHAIN
1
B
ARG
8
0.106
SIDE CHAIN
1
-3.20
0.50
120.30
117.10
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
8
8
8
N
1
10.94
1.10
114.20
125.14
A
A
A
CA
CB
SG
CYS
CYS
CYS
67
67
67
N
1
4.12
0.50
120.30
124.42
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
87
87
87
N
1
3.72
0.50
120.30
124.02
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
87
87
87
N
1
-11.62
1.90
110.30
98.68
B
B
B
N
CA
CB
THR
THR
THR
91
91
91
N
1
A
A
CE2
CD2
TRP
TRP
6
6
0.083
0.012
1.409
1.492
N
1
A
A
CE2
CD2
TRP
TRP
42
42
0.084
0.012
1.409
1.493
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
0.084
0.012
1.409
1.493
N
1
A
PRO
39
-39.89
90.69
1
A
CYS
67
53.06
176.10
0.1900000
0.1900000
1.80
1
1HVR
1.80
0
1870
30
0
1840
0.017
3.50
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
MOLECULAR RECOGNITION OF CYCLIC UREA HIV PROTEASE INHIBITORS
1
N
N
1
N
N
2
N
N
A
ARG
87
A
ARG
87
HELX_P
A
LEU
90
A
LEU
90
1
1
4
B
ARG
87
B
ARG
87
HELX_P
B
ILE
93
B
ILE
93
1
2
7
ASPARTYL PROTEASE
ASPARTYL PROTEASE, HYDROLASE, ACID PROTEINASE
POL_HV1H2
UNP
1
1
P04585
FFREDLAFLQGKAREFSSEQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQVTLWQRPLVTIKIGGQLKEALL
DTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPISPI
ETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQ
DFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMT
KILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIV
LPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDL
IAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEY
WQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLDGI
DKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIE
AEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQV
RDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRNPLWKGPAKLLWKG
EGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED
57
155
1HWR
1
99
P04585
A
1
1
99
57
155
1HWR
1
99
P04585
B
1
1
99
1
CYS
conflict
ALA
95
1HWR
A
P04585
UNP
151
95
2
CYS
conflict
ALA
95
1HWR
B
P04585
UNP
151
95
4
3
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
GLN
18
A
GLN
18
A
LEU
23
A
LEU
23
A
LEU
10
A
LEU
10
A
ILE
15
A
ILE
15
A
ILE
62
A
ILE
62
A
ILE
66
A
ILE
66
A
LYS
70
A
LYS
70
A
GLY
73
A
GLY
73
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
A
GLY
52
A
GLY
52
A
TYR
59
A
TYR
59
A
VAL
75
A
VAL
75
A
GLY
78
A
GLY
78
B
GLN
18
B
GLN
18
B
LEU
23
B
LEU
23
B
LEU
10
B
LEU
10
B
ILE
15
B
ILE
15
B
ILE
62
B
ILE
62
B
ILE
66
B
ILE
66
B
HIS
69
B
HIS
69
B
GLY
73
B
GLY
73
B
VAL
32
B
VAL
32
B
GLU
34
B
GLU
34
B
VAL
75
B
VAL
75
B
GLY
78
B
GLY
78
B
PHE
53
B
PHE
53
B
TYR
59
B
TYR
59
B
LYS
43
B
LYS
43
B
GLY
48
B
GLY
48
BINDING SITE FOR RESIDUE 216 B 216
B
216
216
Software
13
A
ASP
25
A
ASP
25
13
1_555
A
GLY
27
A
GLY
27
13
1_555
A
ALA
28
A
ALA
28
13
1_555
A
ILE
50
A
ILE
50
13
1_555
A
PRO
81
A
PRO
81
13
1_555
A
VAL
82
A
VAL
82
13
1_555
B
ARG
8
B
ARG
8
13
1_555
B
ASP
25
B
ASP
25
13
1_555
B
GLY
27
B
GLY
27
13
1_555
B
ALA
28
B
ALA
28
13
1_555
B
GLY
49
B
GLY
49
13
1_555
B
ILE
50
B
ILE
50
13
1_555
B
PRO
81
B
PRO
81
13
1_555
169
P 61