0.013096
0.007561
0.000000
0.000000
0.015122
0.000000
0.000000
0.000000
0.010925
0.00000
0.00000
0.00000
Chirgadze, N.Y.
Schevitz, R.W.
Wery, J.-P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
76.360
76.360
91.530
C22 H24 N2 O4
380.437
4-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-BUTYRIC ACID
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
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
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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
2
458
465
10.1038/nsb0695-458
7664108
Structure-based design of the first potent and selective inhibitor of human non-pancreatic secretory phospholipase A2.
1995
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298.0
1
IMAGE PLATE
1994-11-03
RIGAKU RAXIS IIC
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
ROTATING ANODE
RIGAKU RU200
13945.012
PROTEIN (PHOSPHOLIPASE A2)
3.1.1.4
1
man
polymer
40.078
CALCIUM ION
2
syn
non-polymer
380.437
4-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-BUTYRIC ACID
1
syn
non-polymer
18.015
water
38
nat
water
no
no
NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQ
DSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC
NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQ
DSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC
A
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
human
Homo
sample
9606
Homo sapiens
1
2.8
56
VAPOR DIFFUSION
7.0
10 mg/ml of protein; 50 mM buffer (MES or MOPS), 1% pyridine., pH 7.0, VAPOR DIFFUSION, temperature 297K
297
repository
Initial release
Version format compliance
Version format compliance
Database references
1
0
1999-11-12
1
1
2008-04-27
1
2
2011-07-13
1
3
2012-02-29
HUMAN S-PLA2 IN COMPLEX WITH INDOLE 8
HUMAN S-PLA2 IN COMPLEX WITH INDOLE 3
RCSB
Y
RCSB
1999-11-02
REL
CA
CALCIUM ION
6IN
4-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-BUTYRIC ACID
HOH
water
CA
198
2
CA
CA
198
A
CA
199
2
CA
CA
199
A
6IN
200
3
6IN
6IN
200
A
HOH
201
4
HOH
HOH
201
A
HOH
202
4
HOH
HOH
202
A
HOH
203
4
HOH
HOH
203
A
HOH
204
4
HOH
HOH
204
A
HOH
205
4
HOH
HOH
205
A
HOH
206
4
HOH
HOH
206
A
HOH
207
4
HOH
HOH
207
A
HOH
208
4
HOH
HOH
208
A
HOH
209
4
HOH
HOH
209
A
HOH
210
4
HOH
HOH
210
A
HOH
211
4
HOH
HOH
211
A
HOH
212
4
HOH
HOH
212
A
HOH
213
4
HOH
HOH
213
A
HOH
214
4
HOH
HOH
214
A
HOH
215
4
HOH
HOH
215
A
HOH
217
4
HOH
HOH
217
A
HOH
218
4
HOH
HOH
218
A
HOH
219
4
HOH
HOH
219
A
HOH
220
4
HOH
HOH
220
A
HOH
221
4
HOH
HOH
221
A
HOH
222
4
HOH
HOH
222
A
HOH
223
4
HOH
HOH
223
A
HOH
224
4
HOH
HOH
224
A
HOH
225
4
HOH
HOH
225
A
HOH
226
4
HOH
HOH
226
A
HOH
227
4
HOH
HOH
227
A
HOH
228
4
HOH
HOH
228
A
HOH
230
4
HOH
HOH
230
A
HOH
231
4
HOH
HOH
231
A
HOH
232
4
HOH
HOH
232
A
HOH
233
4
HOH
HOH
233
A
HOH
235
4
HOH
HOH
235
A
HOH
236
4
HOH
HOH
236
A
HOH
237
4
HOH
HOH
237
A
HOH
238
4
HOH
HOH
238
A
HOH
239
4
HOH
HOH
239
A
HOH
240
4
HOH
HOH
240
A
HOH
342
4
HOH
HOH
342
A
ASN
1
n
1
ASN
1
A
LEU
2
n
2
LEU
2
A
VAL
3
n
3
VAL
3
A
ASN
4
n
4
ASN
4
A
PHE
5
n
5
PHE
5
A
HIS
6
n
6
HIS
6
A
ARG
7
n
7
ARG
7
A
MET
8
n
8
MET
8
A
ILE
9
n
9
ILE
9
A
LYS
10
n
10
LYS
10
A
LEU
11
n
11
LEU
11
A
THR
12
n
12
THR
12
A
THR
13
n
13
THR
13
A
GLY
14
n
14
GLY
14
A
LYS
15
n
15
LYS
15
A
GLU
16
n
16
GLU
16
A
ALA
17
n
17
ALA
17
A
ALA
18
n
18
ALA
18
A
LEU
19
n
19
LEU
19
A
SER
20
n
20
SER
20
A
TYR
21
n
21
TYR
21
A
GLY
22
n
22
GLY
22
A
PHE
23
n
23
PHE
23
A
TYR
24
n
24
TYR
24
A
GLY
25
n
25
GLY
25
A
CYS
26
n
26
CYS
26
A
HIS
27
n
27
HIS
27
A
CYS
28
n
28
CYS
28
A
GLY
29
n
29
GLY
29
A
VAL
30
n
30
VAL
30
A
GLY
31
n
31
GLY
31
A
GLY
32
n
32
GLY
32
A
ARG
33
n
33
ARG
33
A
GLY
34
n
34
GLY
34
A
SER
35
n
35
SER
35
A
PRO
36
n
36
PRO
36
A
LYS
37
n
37
LYS
37
A
ASP
38
n
38
ASP
38
A
ALA
39
n
39
ALA
39
A
THR
40
n
40
THR
40
A
ASP
41
n
41
ASP
41
A
ARG
42
n
42
ARG
42
A
CYS
43
n
43
CYS
43
A
CYS
44
n
44
CYS
44
A
VAL
45
n
45
VAL
45
A
THR
46
n
46
THR
46
A
HIS
47
n
47
HIS
47
A
ASP
48
n
48
ASP
48
A
CYS
49
n
49
CYS
49
A
CYS
50
n
50
CYS
50
A
TYR
51
n
51
TYR
51
A
LYS
52
n
52
LYS
52
A
ARG
53
n
53
ARG
53
A
LEU
54
n
54
LEU
54
A
GLU
55
n
55
GLU
55
A
LYS
56
n
56
LYS
56
A
ARG
57
n
57
ARG
57
A
GLY
58
n
58
GLY
58
A
CYS
59
n
59
CYS
59
A
GLY
60
n
60
GLY
60
A
THR
61
n
61
THR
61
A
LYS
62
n
62
LYS
62
A
PHE
63
n
63
PHE
63
A
LEU
64
n
64
LEU
64
A
SER
65
n
65
SER
65
A
TYR
66
n
66
TYR
66
A
LYS
67
n
67
LYS
67
A
PHE
68
n
68
PHE
68
A
SER
69
n
69
SER
69
A
ASN
70
n
70
ASN
70
A
SER
71
n
71
SER
71
A
GLY
72
n
72
GLY
72
A
SER
73
n
73
SER
73
A
ARG
74
n
74
ARG
74
A
ILE
75
n
75
ILE
75
A
THR
76
n
76
THR
76
A
CYS
77
n
77
CYS
77
A
ALA
78
n
78
ALA
78
A
LYS
79
n
79
LYS
79
A
GLN
80
n
80
GLN
80
A
ASP
81
n
81
ASP
81
A
SER
82
n
82
SER
82
A
CYS
83
n
83
CYS
83
A
ARG
84
n
84
ARG
84
A
SER
85
n
85
SER
85
A
GLN
86
n
86
GLN
86
A
LEU
87
n
87
LEU
87
A
CYS
88
n
88
CYS
88
A
GLU
89
n
89
GLU
89
A
CYS
90
n
90
CYS
90
A
ASP
91
n
91
ASP
91
A
LYS
92
n
92
LYS
92
A
ALA
93
n
93
ALA
93
A
ALA
94
n
94
ALA
94
A
ALA
95
n
95
ALA
95
A
THR
96
n
96
THR
96
A
CYS
97
n
97
CYS
97
A
PHE
98
n
98
PHE
98
A
ALA
99
n
99
ALA
99
A
ARG
100
n
100
ARG
100
A
ASN
101
n
101
ASN
101
A
LYS
102
n
102
LYS
102
A
THR
103
n
103
THR
103
A
THR
104
n
104
THR
104
A
TYR
105
n
105
TYR
105
A
ASN
106
n
106
ASN
106
A
LYS
107
n
107
LYS
107
A
LYS
108
n
108
LYS
108
A
TYR
109
n
109
TYR
109
A
GLN
110
n
110
GLN
110
A
TYR
111
n
111
TYR
111
A
TYR
112
n
112
TYR
112
A
SER
113
n
113
SER
113
A
ASN
114
n
114
ASN
114
A
LYS
115
n
115
LYS
115
A
HIS
116
n
116
HIS
116
A
CYS
117
n
117
CYS
117
A
ARG
118
n
118
ARG
118
A
GLY
119
n
119
GLY
119
A
SER
120
n
120
SER
120
A
THR
121
n
121
THR
121
A
PRO
122
n
122
PRO
122
A
ARG
123
n
123
ARG
123
A
CYS
124
n
124
CYS
124
A
author_defined_assembly
1
monomeric
A
HIS
27
A
O
HIS
27
1_555
A
CA
198
B
CA
CA
1_555
A
ASP
48
A
OD1
ASP
48
1_555
97.2
A
HIS
27
A
O
HIS
27
1_555
A
CA
198
B
CA
CA
1_555
A
GLY
31
A
O
GLY
31
1_555
91.5
A
ASP
48
A
OD1
ASP
48
1_555
A
CA
198
B
CA
CA
1_555
A
GLY
31
A
O
GLY
31
1_555
89.1
A
HIS
27
A
O
HIS
27
1_555
A
CA
198
B
CA
CA
1_555
A
ASP
48
A
OD2
ASP
48
1_555
114.4
A
ASP
48
A
OD1
ASP
48
1_555
A
CA
198
B
CA
CA
1_555
A
ASP
48
A
OD2
ASP
48
1_555
48.9
A
GLY
31
A
O
GLY
31
1_555
A
CA
198
B
CA
CA
1_555
A
ASP
48
A
OD2
ASP
48
1_555
131.2
A
HIS
27
A
O
HIS
27
1_555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O40
6IN
1_555
74.9
A
ASP
48
A
OD1
ASP
48
1_555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O40
6IN
1_555
112.9
A
GLY
31
A
O
GLY
31
1_555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O40
6IN
1_555
155.1
A
ASP
48
A
OD2
ASP
48
1_555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O40
6IN
1_555
73.8
A
HIS
27
A
O
HIS
27
1_555
A
CA
198
B
CA
CA
1_555
A
GLY
29
A
O
GLY
29
1_555
94.1
A
ASP
48
A
OD1
ASP
48
1_555
A
CA
198
B
CA
CA
1_555
A
GLY
29
A
O
GLY
29
1_555
168.7
A
GLY
31
A
O
GLY
31
1_555
A
CA
198
B
CA
CA
1_555
A
GLY
29
A
O
GLY
29
1_555
90.4
A
ASP
48
A
OD2
ASP
48
1_555
A
CA
198
B
CA
CA
1_555
A
GLY
29
A
O
GLY
29
1_555
125.5
A
6IN
200
D
O40
6IN
1_555
A
CA
198
B
CA
CA
1_555
A
GLY
29
A
O
GLY
29
1_555
70.3
A
HIS
27
A
O
HIS
27
1_555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O54
6IN
1_555
168.8
A
ASP
48
A
OD1
ASP
48
1_555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O54
6IN
1_555
85.4
A
GLY
31
A
O
GLY
31
1_555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O54
6IN
1_555
77.7
A
ASP
48
A
OD2
ASP
48
1_555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O54
6IN
1_555
75.5
A
6IN
200
D
O40
6IN
1_555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O54
6IN
1_555
114.2
A
GLY
29
A
O
GLY
29
1_555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O54
6IN
1_555
83.4
A
ASN
114
A
OD1
ASN
114
1_555
A
CA
199
C
CA
CA
1_555
A
TYR
112
A
O
TYR
112
1_555
91.4
A
ASN
114
A
OD1
ASN
114
1_555
A
CA
199
C
CA
CA
1_555
A
PHE
23
A
O
PHE
23
1_555
170.1
A
TYR
112
A
O
TYR
112
1_555
A
CA
199
C
CA
CA
1_555
A
PHE
23
A
O
PHE
23
1_555
83.0
A
ASN
114
A
OD1
ASN
114
1_555
A
CA
199
C
CA
CA
1_555
A
GLY
25
A
O
GLY
25
1_555
81.5
A
TYR
112
A
O
TYR
112
1_555
A
CA
199
C
CA
CA
1_555
A
GLY
25
A
O
GLY
25
1_555
86.2
A
PHE
23
A
O
PHE
23
1_555
A
CA
199
C
CA
CA
1_555
A
GLY
25
A
O
GLY
25
1_555
89.9
A
ASN
114
A
OD1
ASN
114
1_555
A
CA
199
C
CA
CA
1_555
A
HOH
237
E
O
HOH
12_556
84.6
A
TYR
112
A
O
TYR
112
1_555
A
CA
199
C
CA
CA
1_555
A
HOH
237
E
O
HOH
12_556
155.7
A
PHE
23
A
O
PHE
23
1_555
A
CA
199
C
CA
CA
1_555
A
HOH
237
E
O
HOH
12_556
97.1
A
GLY
25
A
O
GLY
25
1_555
A
CA
199
C
CA
CA
1_555
A
HOH
237
E
O
HOH
12_556
69.5
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
SER
71
A
N
SER
71
A
O
ARG
74
A
O
ARG
74
1
A
THR
61
-133.79
-72.06
1
A
ASP
81
-40.66
154.70
1
A
TYR
111
-118.13
52.72
0.24
0.196
0.196
2.80
30.00
209
3933
5.4
87.9
RANDOM
0.001
1000000
1
2.000
2.80
30.00
38
1034
30
0
966
0.010
1.33
24.20
0.736
0.284
0.299
2.93
24
436
8
5.4
94.7
23.60
2.800
30.000
1DB5
4159
0.079
1
14.2000
2.500
97.8
0.274
2.80
2.85
3.3
1
2.50
99.5
data reduction
DENZO
data scaling
SCALEPACK
model building
X-PLOR
refinement
X-PLOR
98.0
phasing
X-PLOR
PHOSPHOLIPASE A2 (E.C.3.1.1.4)
HUMAN S-PLA2 IN COMPLEX WITH INDOLE 6
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
ASN
1
A
ASN
1
HELX_P
A
GLY
14
A
GLY
14
1
1
14
A
GLU
16
A
GLU
16
HELX_P
A
GLY
22
A
GLY
22
1
2
7
A
ASP
38
A
ASP
38
HELX_P
A
ARG
57
A
ARG
57
1
3
20
A
ASP
81
A
ASP
81
HELX_P
A
ASN
101
A
ASN
101
1
4
21
A
LYS
102
A
LYS
102
HELX_P
A
TYR
105
A
TYR
105
5
5
4
A
ASN
106
A
ASN
106
HELX_P
A
GLN
110
A
GLN
110
5
6
5
A
SER
113
A
SER
113
HELX_P
A
CYS
117
A
CYS
117
5
7
5
disulf
2.028
A
CYS
26
A
SG
CYS
26
1_555
A
CYS
117
A
SG
CYS
117
1_555
disulf
2.030
A
CYS
28
A
SG
CYS
28
1_555
A
CYS
44
A
SG
CYS
44
1_555
disulf
2.033
A
CYS
43
A
SG
CYS
43
1_555
A
CYS
97
A
SG
CYS
97
1_555
disulf
2.023
A
CYS
49
A
SG
CYS
49
1_555
A
CYS
124
A
SG
CYS
124
1_555
disulf
2.021
A
CYS
50
A
SG
CYS
50
1_555
A
CYS
90
A
SG
CYS
90
1_555
disulf
2.023
A
CYS
59
A
SG
CYS
59
1_555
A
CYS
83
A
SG
CYS
83
1_555
disulf
2.034
A
CYS
77
A
SG
CYS
77
1_555
A
CYS
88
A
SG
CYS
88
1_555
metalc
2.394
A
CA
198
B
CA
CA
1_555
A
HIS
27
A
O
HIS
27
1_555
metalc
2.530
A
CA
198
B
CA
CA
1_555
A
ASP
48
A
OD1
ASP
48
1_555
metalc
2.398
A
CA
198
B
CA
CA
1_555
A
GLY
31
A
O
GLY
31
1_555
metalc
2.752
A
CA
198
B
CA
CA
1_555
A
ASP
48
A
OD2
ASP
48
1_555
metalc
2.559
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O40
6IN
1_555
metalc
2.437
A
CA
198
B
CA
CA
1_555
A
GLY
29
A
O
GLY
29
1_555
metalc
2.555
A
CA
198
B
CA
CA
1_555
A
6IN
200
D
O54
6IN
1_555
metalc
2.640
A
CA
199
C
CA
CA
1_555
A
ASN
114
A
OD1
ASN
114
1_555
metalc
2.548
A
CA
199
C
CA
CA
1_555
A
TYR
112
A
O
TYR
112
1_555
metalc
2.648
A
CA
199
C
CA
CA
1_555
A
PHE
23
A
O
PHE
23
1_555
metalc
2.912
A
CA
199
C
CA
CA
1_555
A
GLY
25
A
O
GLY
25
1_555
metalc
2.773
A
CA
199
C
CA
CA
1_555
A
HOH
237
E
O
HOH
12_556
HYDROLASE/HYDROLASE INHIBITOR
S-PLA2; STRUCTURE-BASED DRUG DESIGN, HYDROLASE/HYDROLASE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR complex
PA2GA_HUMAN
UNP
1
P14555
21
144
1DB5
1
124
P14555
A
1
1
124
2
anti-parallel
A
PHE
68
A
PHE
68
A
SER
71
A
SER
71
A
ARG
74
A
ARG
74
A
CYS
77
A
CYS
77
BINDING SITE FOR RESIDUE CA A 198
Software
5
BINDING SITE FOR RESIDUE CA A 199
Software
5
BINDING SITE FOR RESIDUE 6IN A 200
Software
17
A
HIS
27
A
HIS
27
5
1_555
A
GLY
29
A
GLY
29
5
1_555
A
GLY
31
A
GLY
31
5
1_555
A
ASP
48
A
ASP
48
5
1_555
A
6IN
200
D
6IN
5
1_555
A
PHE
23
A
PHE
23
5
1_555
A
GLY
25
A
GLY
25
5
1_555
A
TYR
112
A
TYR
112
5
1_555
A
ASN
114
A
ASN
114
5
1_555
A
HOH
237
E
HOH
5
12_556
A
LEU
2
A
LEU
2
17
1_555
A
HIS
6
A
HIS
6
17
1_555
A
LEU
19
A
LEU
19
17
12_556
A
TYR
21
A
TYR
21
17
1_555
A
HIS
27
A
HIS
27
17
1_555
A
CYS
28
A
CYS
28
17
1_555
A
GLY
29
A
GLY
29
17
1_555
A
VAL
30
A
VAL
30
17
1_555
A
GLY
31
A
GLY
31
17
1_555
A
CYS
44
A
CYS
44
17
1_555
A
HIS
47
A
HIS
47
17
1_555
A
ASP
48
A
ASP
48
17
1_555
A
TYR
51
A
TYR
51
17
1_555
A
LYS
52
A
LYS
52
17
1_555
A
LYS
62
A
LYS
62
17
1_555
A
CA
198
B
CA
17
1_555
A
HOH
236
E
HOH
17
1_555
178
P 61 2 2