Checking the Ki values of the used X-ray structures for the
urokinase COMBINE model
For some of the Ki values (given in M) a inconsistents could be found.
After checking the corresponding articles the old Ki values (bold
numbers of column 'alt Ki exp' in table) were changed (see column neu
Ki). The ligands were grouped into three parts based on the different
research groups (yellow: Katz et al., blue: Strzebecher et al., grey:
Wendt et al.). The values for A25 and A28 were identified as outliers.
The ligands can split into the following groups (ligands in brackets
should not used because of potential inconsistancy of the Ki values):
Katz
Strzebecher
Wendt
# 12
(13)
#
6 (7)
#
9 (10)
A04
(A20)
(A29)
A12
A25
A30
A13
A26
A31
A14
A28
A32
A15
A39
A33
A16
A40
A34
A17
A41
A35
A18
A36
A19
A37
(A20)
A38
A21
A23
A24
ID
residue
PDB
PDB Ref
#
dGexp
alt Kiexp
neu Ki
MOAD
Ki
conditions
KiRef
Ki
conditions
KiRef
Ki
conditions
KiRef
14
A04
1o5a
JMB2004,344
8696
Ala190
-9.739
0.072
0.072
0.072
pH 7,4
JMB2003,93
8
A12
1gi8
-6.886
8.9
7.2
8.9
pH 7,4
JMB2003,93
5.5
pH 7,4, -Zn
JMC2001,44
2.65
pH 7,4, +Zn
JMC2001,44
12
A13
1gi9
6669
-7.12
6
4.95
1.1
6
pH 7,4
JMB2003,93
3.9
pH 7,4, -Zn
JMC2001,44
1.1
Ki min,pH 8
JMB2001,307
13
A14
1gjb
7806
-8.654
0.45
0.425
0.45
0.45
pH 7,4, EDTA
JMB2003,93
0.4
pH 7.4, -Zn
JMC2001,44
0.54
pH 7,4, +Zn
JMC2001,44
1gjc
8696
-8.654
0.425
0.008
0.45
pH 7,4, EDTA
JMB2003,93
0.4
pH 7.4, -Zn
JMC2001,44
0.54
pH 7,4, +Zn
JMC2001,44
2
A15
1o3p
10655
-9.077
0.22
0.22
0.22
0.22
pH 7.4
JMB2003,93
4
A16
1gj8
10950
-9.488
0.11
0.11
0.11
0.11
pH 7.4
JMB2003,93
0.11
pH 7.4
ChemBio2001,8
2
pH 8.2, +Zn
ChemBio2001,8
0.16
pH 8.2, EDTA
ChemBio2001,8
7
A17
1o5c
11092
-10.2
0.033
0.033
0.033
pH 7.4
JMB2003,93
1
A18
1gj7
10302
-10.75
0.013
0.011
0.009
0.013
pH 7.4
JMB2003,93
0.009
pH 7.4, EDTA
ChemBio2001,8
0.008
-Zn
JMC2001,44
0.01
+Zn
JMC2001,44
159
A19
1c5x
6860
-9.105
0.21
0.21
0.21
BioorgMedChem2002,12
0.21
ChemBio2000,7
1c5w
6860
-9.105
0.21
BioorgMedChem2002,12
0.21
ChemBio2000,7
105b
6860
-9.105
0.21
BioorgMedChem2002,12
0.21
ChemBio2000,7
160
A20
1c5z
benzamidine
-7.228
5
97
180
5
pH 7.8 min
JMB2001,307
180
JMB2000,301
97
ChemBio2000,7
1f5k
benzamidine
-7.228
180
180
5
pH 7.8 min
JMB2001,307
180
JMB2000,301
97
ChemBio2000,7
161
A21
1c5y
7538
-5.727
63
63
63
ChemBio2000,7
162
A22
1gi7
10273
-6.147
31
31
31
31
pH 5.7 min
JMB2001,307
163
A23
1gjd
11421
-7.12
6
6
6
6
pH 7.4, EDTA
ChemBio2000,7
164
A24
1gja
7136
-7.39
3.8
3.8
3.8
3.8
pH 7.4, EDTA
ChemBio2000,8
165
A25
1ejn
AGB
-7.662
2.4
2.4
2.4
2.4
PNAS2000,97
166
A26
1f5l
amiloride
-7.193
5.3
5.3
5.3
JMB2000,301
A27
1fv9
?
167
A28
1f92
UKI-1D
-8.445
0.64
0.64
0.64
JMB2000,301
168
A29
1sqa
UI1/23b
-12.55
0.00062
0.00062
0.62
0.00062
BioorgMEDChem2004,14
169
A30
1sqo
UI2/2
-10.17
0.035
0.035
0.035
0.035
BioorgMEDChem2004,15
170
A31
1sqt
12b
-8.454
0.63
0.63
0.63
0.63
BioorgMEDChem2004,16
171
A32
1owd
56a
-9.324
0.145
0.0063
6.3
0.0063
JMC2004,47
172
A33
1owe
6
-8.453
0.631
0.631
0.631
0.631
JMC2004,48
173
A34
1owh
25
-10.09
0.04
0.04
0.631
0.04
JMC2004,49
174
A35
1owi
34d
-9.521
0.104
0.104
0.104
JMC2004,50
175
A36
1owj
43a
-9.979
0.048
0.048
0.048
JMC2004,51
176
A37
1owk
47a
-10.4
0.0235
0.035
0.035
JMC2004,52
177
A38
1u6q
19a
-8.021
1.31
1.31
1.31
BioorgMedChem2005,15
178
A39
1vja
26
-10.5
0.02
0.02
0.02
0.02
JBC2004,279
179
A40
1vj9
27
-10.3
0.028
0.028
0.028
0.028
JBC2004,280
180
A41
1sc8
1
-6.817
10
0.036
0.036
0.036
JBC2004,281
A42
1gj9
134
0.011
?
Katz
Katz
JMB2004,344
Katz
Katz
JMB2003,93
Katz
Verner
JMC2001,44
Katz
Katz
JMB2001,307
Katz
Katz
JACS
Katz
Katz
ChemBio2001,8
Katz
Spencer
BioorgMedChem2002,12
Strzebecher
Zeslawska
JMB2000,301
Katz
Katz
ChemBio2000,7
Strzebecher
Sperl
PNAS2000,97
Wendt
Wendt
BioorgMEDChem2004,14
Wendt
Wendt
JMC2004,47
Wendt
Bruncko
BioorgMedChem2005,15
Strzebecher
Schweinitz
JBC2004,281
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