0.017837
0.010298
0.000000
0.000000
0.020596
0.000000
0.000000
0.000000
0.009513
0.000000
0.000000
0.000000
0000-0002-8410-3415
Bader, G.
0000-0001-6808-9011
Kessler, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.000
90.000
120.000
56.064
56.064
105.119
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
C23 H18 Cl2 F N3 O2
458.312
(3~{S},3'~{R},3'~{a}~{S},6'~{a}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{a},6~{a}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione
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
O4 S -2
96.063
SULFATE ION
non-polymer
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
DE
ChemMedChem
1860-7187
14
88
93
10.1002/cmdc.201800617
30458062
Targeted Synthesis of Complex Spiro[3H-indole-3,2'-pyrrolidin]-2(1H)-ones by Intramolecular Cyclization of Azomethine Ylides: Highly Potent MDM2-p53 Inhibitors.
2019
100.000
1
N
PIXEL
2013-12-05
DECTRIS PILATUS3 6M
SINGLE WAVELENGTH
M
x-ray
1
1.00000
1.0
X06SA
SLS
1.00000
SYNCHROTRON
SLS BEAMLINE X06SA
11011.923
E3 ubiquitin-protein ligase Mdm2
2.3.2.27
1
man
polymer
458.312
(3~{S},3'~{R},3'~{a}~{S},6'~{a}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{a},6~{a}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione
1
syn
non-polymer
92.094
GLYCEROL
1
syn
non-polymer
96.063
SULFATE ION
2
syn
non-polymer
18.015
water
47
nat
water
Double minute 2 protein,Hdm2,Oncoprotein Mdm2,RING-type E3 ubiquitin transferase Mdm2,p53-binding protein Mdm2
no
no
QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHR
KIYTMIYRNLVVVN
QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHR
KIYTMIYRNLVVVN
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
Human
sample
1
94
MDM2
9606
Homo sapiens
562
Escherichia coli
Biological sequence
1
2.250
45.480
VAPOR DIFFUSION, HANGING DROP
4.5
2.10 M (NH4)2SO4, 0.10 M Na acetate
293
citation
citation_author
citation
citation_author
pdbx_database_proc
database_PDB_remark
reflns
reflns_shell
repository
Initial release
Data collection
Database references
Data collection
Database references
Data collection
1
0
2018-12-19
1
1
2018-12-26
1
2
2019-01-16
1
3
2019-03-06
_citation.title
_citation_author.identifier_ORCID
_citation_author.name
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.year
_citation_author.identifier_ORCID
_database_PDB_remark.text
_reflns.pdbx_Rmerge_I_obs
_reflns_shell.Rmerge_I_obs
N
PDBE
Y
PDBE
2018-11-07
REL
REL
H28
(3~{S},3'~{R},3'~{a}~{S},6'~{a}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{a},6~{a}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione
GOL
GLYCEROL
SO4
SULFATE ION
HOH
water
LIG
1
2
H28
H28
201
A
GOL
1
3
GOL
GOL
202
A
SO4
2
4
SO4
SO4
203
A
SO4
3
4
SO4
SO4
204
A
HOH
36
5
HOH
HOH
301
A
HOH
22
5
HOH
HOH
302
A
HOH
7
5
HOH
HOH
303
A
HOH
23
5
HOH
HOH
304
A
HOH
14
5
HOH
HOH
305
A
HOH
39
5
HOH
HOH
306
A
HOH
19
5
HOH
HOH
307
A
HOH
6
5
HOH
HOH
308
A
HOH
32
5
HOH
HOH
309
A
HOH
30
5
HOH
HOH
310
A
HOH
51
5
HOH
HOH
311
A
HOH
34
5
HOH
HOH
312
A
HOH
16
5
HOH
HOH
313
A
HOH
3
5
HOH
HOH
314
A
HOH
2
5
HOH
HOH
315
A
HOH
20
5
HOH
HOH
316
A
HOH
44
5
HOH
HOH
317
A
HOH
50
5
HOH
HOH
318
A
HOH
41
5
HOH
HOH
319
A
HOH
27
5
HOH
HOH
320
A
HOH
9
5
HOH
HOH
321
A
HOH
53
5
HOH
HOH
322
A
HOH
47
5
HOH
HOH
323
A
HOH
35
5
HOH
HOH
324
A
HOH
26
5
HOH
HOH
325
A
HOH
15
5
HOH
HOH
326
A
HOH
28
5
HOH
HOH
327
A
HOH
24
5
HOH
HOH
328
A
HOH
45
5
HOH
HOH
329
A
HOH
8
5
HOH
HOH
330
A
HOH
5
5
HOH
HOH
331
A
HOH
43
5
HOH
HOH
332
A
HOH
46
5
HOH
HOH
333
A
HOH
13
5
HOH
HOH
334
A
HOH
38
5
HOH
HOH
335
A
HOH
17
5
HOH
HOH
336
A
HOH
11
5
HOH
HOH
337
A
HOH
10
5
HOH
HOH
338
A
HOH
52
5
HOH
HOH
339
A
HOH
12
5
HOH
HOH
340
A
HOH
40
5
HOH
HOH
341
A
HOH
42
5
HOH
HOH
342
A
HOH
48
5
HOH
HOH
343
A
HOH
25
5
HOH
HOH
344
A
HOH
49
5
HOH
HOH
345
A
HOH
33
5
HOH
HOH
346
A
HOH
37
5
HOH
HOH
347
A
GLN
18
n
1
GLN
18
A
ILE
19
n
2
ILE
19
A
PRO
20
n
3
PRO
20
A
ALA
21
n
4
ALA
21
A
SER
22
n
5
SER
22
A
GLU
23
n
6
GLU
23
A
GLN
24
n
7
GLN
24
A
GLU
25
n
8
GLU
25
A
THR
26
n
9
THR
26
A
LEU
27
n
10
LEU
27
A
VAL
28
n
11
VAL
28
A
ARG
29
n
12
ARG
29
A
PRO
30
n
13
PRO
30
A
LYS
31
n
14
LYS
31
A
PRO
32
n
15
PRO
32
A
LEU
33
n
16
LEU
33
A
LEU
34
n
17
LEU
34
A
LEU
35
n
18
LEU
35
A
LYS
36
n
19
LYS
36
A
LEU
37
n
20
LEU
37
A
LEU
38
n
21
LEU
38
A
LYS
39
n
22
LYS
39
A
SER
40
n
23
SER
40
A
VAL
41
n
24
VAL
41
A
GLY
42
n
25
GLY
42
A
ALA
43
n
26
ALA
43
A
GLN
44
n
27
GLN
44
A
LYS
45
n
28
LYS
45
A
ASP
46
n
29
ASP
46
A
THR
47
n
30
THR
47
A
TYR
48
n
31
TYR
48
A
THR
49
n
32
THR
49
A
MET
50
n
33
MET
50
A
LYS
51
n
34
LYS
51
A
GLU
52
n
35
GLU
52
A
VAL
53
n
36
VAL
53
A
LEU
54
n
37
LEU
54
A
PHE
55
n
38
PHE
55
A
TYR
56
n
39
TYR
56
A
LEU
57
n
40
LEU
57
A
GLY
58
n
41
GLY
58
A
GLN
59
n
42
GLN
59
A
TYR
60
n
43
TYR
60
A
ILE
61
n
44
ILE
61
A
MET
62
n
45
MET
62
A
THR
63
n
46
THR
63
A
LYS
64
n
47
LYS
64
A
ARG
65
n
48
ARG
65
A
LEU
66
n
49
LEU
66
A
TYR
67
n
50
TYR
67
A
ASP
68
n
51
ASP
68
A
GLU
69
n
52
GLU
69
A
LYS
70
n
53
LYS
70
A
GLN
71
n
54
GLN
71
A
GLN
72
n
55
GLN
72
A
HIS
73
n
56
HIS
73
A
ILE
74
n
57
ILE
74
A
VAL
75
n
58
VAL
75
A
TYR
76
n
59
TYR
76
A
CYS
77
n
60
CYS
77
A
SER
78
n
61
SER
78
A
ASN
79
n
62
ASN
79
A
ASP
80
n
63
ASP
80
A
LEU
81
n
64
LEU
81
A
LEU
82
n
65
LEU
82
A
GLY
83
n
66
GLY
83
A
ASP
84
n
67
ASP
84
A
LEU
85
n
68
LEU
85
A
PHE
86
n
69
PHE
86
A
GLY
87
n
70
GLY
87
A
VAL
88
n
71
VAL
88
A
PRO
89
n
72
PRO
89
A
SER
90
n
73
SER
90
A
PHE
91
n
74
PHE
91
A
SER
92
n
75
SER
92
A
VAL
93
n
76
VAL
93
A
LYS
94
n
77
LYS
94
A
GLU
95
n
78
GLU
95
A
HIS
96
n
79
HIS
96
A
ARG
97
n
80
ARG
97
A
LYS
98
n
81
LYS
98
A
ILE
99
n
82
ILE
99
A
TYR
100
n
83
TYR
100
A
THR
101
n
84
THR
101
A
MET
102
n
85
MET
102
A
ILE
103
n
86
ILE
103
A
TYR
104
n
87
TYR
104
A
ARG
105
n
88
ARG
105
A
ASN
106
n
89
ASN
106
A
LEU
107
n
90
LEU
107
A
VAL
108
n
91
VAL
108
A
VAL
109
n
92
VAL
109
A
VAL
110
n
93
VAL
110
A
ASN
111
n
94
ASN
111
A
author_and_software_defined_assembly
PISA
1
monomeric
gel filtration
480
-18
6080
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
TYR
48
A
O
TYR
31
A
N
VAL
28
A
N
VAL
11
A
N
LEU
27
A
N
LEU
10
A
O
VAL
110
A
O
VAL
93
A
N
ASP
68
A
N
ASP
51
A
O
ILE
74
A
O
ILE
57
A
N
VAL
75
A
N
VAL
58
A
O
PHE
91
A
O
PHE
74
1
A
A
CG
CD
LYS
LYS
70
70
0.228
0.034
1.520
1.748
N
1
A
A
CB
CG
GLN
GLN
71
71
0.178
0.027
1.521
1.699
N
1
A
GLN
71
84.13
68.36
73.820
18.2080
9.500
0.0300
0.0200
0.0000
0.0300
0.0000
-0.0500
0.9590
0.9280
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.2392
0.1884
0.1933
1.7700
48.5500
982
8824
10.0000
96.9600
6.0720
0.0900
RANDOM
1
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
0.1410
0.1400
0.8000
0.8000
1.2000
1.7700
48.5500
47
873
25.90
40.34
52
0
774
94
0.011
0.020
846
0.009
0.020
574
1.517
2.062
1156
1.144
3.000
1399
6.549
5.000
97
43.011
23.939
33
12.732
15.000
148
25.184
15.000
4
0.089
0.200
133
0.006
0.021
892
0.001
0.020
164
0.3480
0.0000
0.2950
1.8160
70
525
595
20
95.2000
1.770
48.550
6I3S
9499
0.096
1
23.92
23.100
98.600
0.44
1.800
2.050
1
23.700
97.600
refinement
REFMAC
5.6.0117
data extraction
PDB_EXTRACT
3.24
data reduction
XDS
data scaling
XSCALE
phasing
PHASER
N
E3 ubiquitin-protein ligase Mdm2 (E.C.2.3.2.27)
Crystal structure of MDM2 in complex with compound 13.
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
A
PRO
20
A
PRO
3
HELX_P
A
GLU
25
A
GLU
8
5
AA1
6
A
LYS
31
A
LYS
14
HELX_P
A
SER
40
A
SER
23
1
AA2
10
A
MET
50
A
MET
33
HELX_P
A
LYS
64
A
LYS
47
1
AA3
15
A
ASP
80
A
ASP
63
HELX_P
A
GLY
87
A
GLY
70
1
AA4
8
A
GLU
95
A
GLU
78
HELX_P
A
ARG
105
A
ARG
88
1
AA5
11
LIGASE
Inhibitor, LIGASE
MDM2_HUMAN
UNP
1
18
Q00987
QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHR
KIYTMIYRNLVVVN
18
111
6I3S
18
111
Q00987
A
1
1
94
3
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
48
A
TYR
31
A
THR
49
A
THR
32
A
LEU
27
A
LEU
10
A
PRO
30
A
PRO
13
A
LEU
107
A
LEU
90
A
VAL
110
A
VAL
93
A
TYR
67
A
TYR
50
A
ASP
68
A
ASP
51
A
ILE
74
A
ILE
57
A
TYR
76
A
TYR
59
A
SER
90
A
SER
73
A
SER
92
A
SER
75
binding site for residue H28 A 201
A
H28
201
Software
11
binding site for residue GOL A 202
A
GOL
202
Software
4
binding site for residue SO4 A 203
A
SO4
203
Software
7
binding site for residue SO4 A 204
A
SO4
204
Software
8
A
LEU
54
A
LEU
37
11
1_555
A
GLY
58
A
GLY
41
11
1_555
A
ILE
61
A
ILE
44
11
1_555
A
MET
62
A
MET
45
11
1_555
A
PHE
86
A
PHE
69
11
1_555
A
VAL
93
A
VAL
76
11
1_555
A
HIS
96
A
HIS
79
11
1_555
A
ILE
99
A
ILE
82
11
1_555
A
TYR
100
A
TYR
83
11
1_555
A
HOH
315
F
HOH
11
1_555
A
HOH
320
F
HOH
11
1_555
A
ILE
19
A
ILE
2
4
1_555
A
HIS
96
A
HIS
79
4
1_555
A
TYR
100
A
TYR
83
4
1_555
A
HOH
311
F
HOH
4
1_555
A
GLN
18
A
GLN
1
7
1_555
A
LYS
94
A
LYS
77
7
1_555
A
GLU
95
A
GLU
78
7
1_555
A
HIS
96
A
HIS
79
7
1_555
A
ARG
97
A
ARG
80
7
1_555
A
LYS
98
A
LYS
81
7
1_555
A
HOH
317
F
HOH
7
1_555
A
ILE
19
A
ILE
2
8
6_555
A
PRO
20
A
PRO
3
8
6_555
A
ALA
21
A
ALA
4
8
6_555
A
LYS
51
A
LYS
34
8
12_555
A
LYS
51
A
LYS
34
8
1_555
A
HOH
313
F
HOH
8
1_555
A
HOH
330
F
HOH
8
6_555
A
HOH
336
F
HOH
8
1_555
178
P 61 2 2