Chemical Components in the PDB

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KT5 : Summary

Code

KT5

One-letter code

X

Molecule name

N-{4-4-(2,4-DIAMINO-6-OXO-1,6-DIHYDRO-PYRIMIDIN-5-YL)-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXY-ETHYL)-BUT-2-YL-BENZOYL}-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GLUTAMIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 N-({4-[(1S)-4-(2,4-diamino-6-hydroxypyrimidin-5-yl)-1-(2,2,2-trifluoro-1,1-dihydroxyethyl)butyl]phenyl}carbonyl)-L-gamma-glutamyl-gamma-glutamyl-gamma-glutamyl-gamma-glutamylglutamic acid
OpenEye OEToolkits 1.5.0 (2R)-2-[[(4R)-4-[[(4R)-4-[[(4R)-4-[[(4S)-4-[[4-[(3S)-6-(2,4-diamino-6-hydroxy-pyrimidin-5-yl)-1,1,1-trifluoro-2,2-dihydroxy-hexan-3-yl]phenyl]carbonylamino]-5-hydroxy-5-oxo-pentanoyl]amino]-5-hydroxy-5-oxo-pentanoyl]amino]-5-hydroxy-5-oxo-pentanoyl]amino]-5-hydroxy-5-oxo-pentanoyl]amino]pentanedioic acid

Formula

C42 H54 F3 N9 O20

Formal charge

0

Molecular weight

1061.922 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(NC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)c1ccc(cc1)C(C(O)(O)C(F)(F)F)CCCc2c(O)nc(nc2N)N)CCC(=O)O
SMILES CACTVS 3.341 Nc1nc(N)c(CCC[CH](c2ccc(cc2)C(=O)N[CH](CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)(O)C(F)(F)F)c(O)n1
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1C(CCCc2c(nc(nc2O)N)N)C(C(F)(F)F)(O)O)C(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O
Canonical SMILES CACTVS 3.341 Nc1nc(N)c(CCC[C@@H](c2ccc(cc2)C(=O)N[C@@H](CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)=O)C(O)(O)C(F)(F)F)c(O)n1
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1[C@H](CCCc2c(nc(nc2O)N)N)C(C(F)(F)F)(O)O)C(=O)N[C@@H](CCC(=O)N[C@H](CCC(=O)N[C@H](CCC(=O)N[C@H](CCC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O)C(=O)O

IUPAC InChI

InChI=1S/C42H54F3N9O20/c43-42(44,45)41(73,74)21(3-1-2-20-32(46)53-40(47)54-34(20)62)18-4-6-19(7-5-18)33(61)52-26(39(71)72)11-16-30(58)50-24(37(67)68)9-14-28(56)48-22(35(63)64)8-13-27(55)49-23(36(65)66)10-15-29(57)51-25(38(69)70)12-17-31(59)60/h4-7,21-26,73-74H,1-3,8-17H2,(H,48,56)(H,49,55)(H,50,58)(H,51,57)(H,52,61)(H,59,60)(H,63,64)(H,65,66)(H,67,68)(H,69,70)(H,71,72)(H5,46,47,53,54,62)/t21-,22?,23?,24?,25?,26-/m0/s1

IUPAC InChI key

IWEGOVKIJZGOSL-RCZRCYCLSA-N
KT5

wwPDB Information

Atom count

128 (74 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2003-11-11

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



KT5 : Atoms of Molecule

Total Number of Atoms: 128
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N2A N 2N N N N 0 3.766 6.769 -15.176
2 CD1 C 1CD N N N 0 2.608 6.758 -15.939
3 OEB O 1OE1 N N N 0 1.82 5.818 -16.012
4 CG1 C 1CG N N N 0 2.404 8.076 -16.667
5 CB1 C 1CB N N N 0 1.137 8.113 -17.524
6 CA1 C 1CA S N N 0 0.955 9.429 -18.284
7 C1A C 1C N N N 0 -0.304 9.379 -19.127
8 O11 O 1OXT N N N 0 -0.056 8.923 -20.383
9 O1A O 1O N N N 0 -1.428 9.665 -18.734
10 N1A N 1N N N N 0 0.813 10.559 -17.402
11 C C C N N N 0 1.176 11.847 -17.772
12 O O O N N N 0 1.646 12.155 -18.865
13 C14 C C14 N Y N 0 0.993 12.898 -16.739
14 C15 C C15 N Y N 0 1.796 14.018 -16.778
15 C16 C C16 N Y N 0 1.623 15.006 -15.808
16 C13 C C13 N Y N 0 0.023 12.721 -15.773
17 C12 C C12 N Y N 0 -0.15 13.708 -14.803
18 C11 C C11 N Y N 0 0.65 14.851 -14.821
19 C10 C C10 S N N 0 0.465 15.907 -13.784
20 C5 C C5 N N N 0 1.714 16.145 -12.856
21 C6 C C6 N N N 0 2.129 14.904 -12.07
22 F2 F F2 N N N 0 2.453 13.885 -12.895
23 F1 F F1 N N N 0 1.114 14.48 -11.281
24 F3 F F3 N N N 0 3.186 15.138 -11.265
25 OA2 O OA2 N N N 0 1.372 17.167 -11.911
26 OA1 O OA1 N N N 0 2.808 16.596 -13.652
27 C1 C C1 N N N 0 -0.029 17.266 -14.39
28 C2 C C2 N N N 0 -1.373 17.128 -15.124
29 C3 C C3 N N N 0 -1.84 18.442 -15.762
30 C4 C C4 N Y N 0 -3.197 18.349 -16.413
31 C7 C C7 N Y N 0 -4.353 18.611 -15.726
32 N8 N N8 N N N 0 -4.271 18.983 -14.361
33 C9 C C9 N Y N 0 -3.323 17.993 -17.729
34 O1 O O1 N N N 0 -2.214 17.714 -18.485
35 N3 N N3 N Y N 0 -4.514 17.896 -18.355
36 C8 C C8 N Y N 0 -5.584 18.177 -17.587
37 N2 N N2 N N N 0 -6.848 18.086 -18.209
38 N1 N N1 N Y N 0 -5.577 18.534 -16.288
39 OEF O 5OE1 N N N 0 3.767 -2.97 -10.076
40 OEP O 5OE2 N N N 0 5.206 -1.771 -11.361
41 CD5 C 5CD N N N 0 4.065 -1.928 -10.646
42 CG5 C 5CG N N N 0 3.204 -0.69 -10.642
43 CB5 C 5CB N N N 0 1.955 -0.806 -9.764
44 CA5 C 5CA R N N 0 1.09 0.46 -9.645
45 C5A C 5C N N N 0 0.474 0.861 -10.973
46 O5 O 5O N N N 0 -0.289 0.173 -11.639
47 O12 O 5OXT N N N 0 0.87 2.101 -11.363
48 N5 N 5N N N N 0 1.84 1.586 -9.14
49 OEE O 4OE1 N N N 0 1.426 1.216 -6.886
50 CD4 C 4CD N N N 0 1.944 1.871 -7.786
51 CG4 C 4CG N N N 0 2.815 3.091 -7.536
52 CB4 C 4CB N N N 0 2.961 3.446 -6.055
53 CA4 C 4CA R N N 0 3.808 4.697 -5.81
54 C4A C 4C N N N 0 3.885 4.997 -4.326
55 O4 O 4O N N N 0 3.067 5.652 -3.694
56 O13 O 4OXT N N N 0 5.014 4.49 -3.765
57 N4 N 4N N N N 0 3.249 5.872 -6.438
58 OED O 3OE1 N N N 0 5.245 7.026 -6.708
59 CD3 C 3CD N N N 0 4.027 6.949 -6.838
60 CG3 C 3CG N N N 0 3.187 8.032 -7.495
61 CB3 C 3CB N N N 0 4.001 9.243 -7.955
62 O14 O 3OXT N N N 0 6.967 10.303 -8.749
63 CA3 C 3CA R N N 0 5.057 8.902 -9.01
64 C3A C 3C N N N 0 5.801 10.153 -9.431
65 O3 O 3O N N N 0 5.441 10.928 -10.309
66 N3A N 3N N N N 0 4.476 8.346 -10.21
67 OEC O 2OE1 N N N 0 6.324 7.103 -10.869
68 CD2 C 2CD N N N 0 5.169 7.483 -11.047
69 CG2 C 2CG N N N 0 4.312 7.028 -12.216
70 CB2 C 2CB N N N 0 5.033 6.073 -13.169
71 CA2 C 2CA R N N 0 4.177 5.647 -14.365
72 C2A C 2C N N N 0 4.967 4.725 -15.273
73 O2 O 2O N N N 0 5.714 5.088 -16.172
74 O15 O 2OXT N N N 0 4.714 3.416 -15.01
75 H2 H 2H N N N 0 4.349 7.601 -15.188
76 HB21 H 1HB2 N N N 0 1.147 7.273 -18.231
77 HG11 H 1HG1 N N N 0 3.289 8.297 -17.274
78 HG21 H 1HG2 N N N 0 2.332 8.856 -15.899
79 HB11 H 1HB1 N N N 0 0.271 7.95 -16.868
80 HA1A H 1HA N N N 0 1.81 9.655 -18.929
81 HXT1 H 1HXT N N N 0 -0.844 8.838 -20.96
82 H1 H 1H N N N 0 0.49 10.373 -16.456
83 H15 H H15 N N N 0 2.558 14.149 -17.542
84 H16 H H16 N N N 0 2.251 15.893 -15.829
85 H13 H H13 N N N 0 -0.605 11.834 -15.749
86 H12 H H12 N N N 0 -0.911 13.579 -14.038
87 H10 H H10 N N N 0 -0.35 15.605 -13.092
88 HA2 H HA2 N N N 0 1.965 17.08 -11.146
89 HA1 H HA1 N N N 0 3.631 16.384 -13.181
90 H11 H 1H1 N N N 0 -0.152 18.015 -13.598
91 H12A H 2H1 N N N 0 0.73 17.663 -15.074
92 H21 H 1H2 N N N 0 -1.312 16.346 -15.889
93 H22 H 2H2 N N N 0 -2.136 16.807 -14.404
94 H31 H 1H3 N N N 0 -1.093 18.787 -16.488
95 H32 H 2H3 N N N 0 -1.885 19.22 -14.989
96 HN81 H 1HN8 N N N 0 -5.015 19.511 -13.961
97 HN82 H 2HN8 N N N 0 -3.432 18.789 -13.859
98 HO1 H HO1 N N N 0 -2.432 17.785 -19.425
99 HN21 H 1HN2 N N N 0 -7.317 18.925 -18.483
100 HN22 H 2HN2 N N N 0 -7.293 17.194 -18.278
101 HE25 H 5HE2 N N N 0 5.789 -2.559 -11.395
102 HG15 H 5HG1 N N N 0 2.942 -0.447 -11.677
103 HG25 H 5HG2 N N N 0 3.829 0.141 -10.291
104 HB15 H 5HB1 N N N 0 1.327 -1.633 -10.118
105 HB25 H 5HB2 N N N 0 2.288 -1.091 -8.758
106 HA5 H 5HA N N N 0 0.271 0.273 -8.939
107 HXT5 H 5HXT N N N 0 0.501 2.409 -12.219
108 H5 H 5H N N N 0 2.31 2.195 -9.803
109 HG14 H 4HG1 N N N 0 2.419 3.942 -8.101
110 HG24 H 4HG2 N N N 0 3.808 2.862 -7.943
111 HB14 H 4HB1 N N N 0 3.418 2.591 -5.538
112 HB24 H 4HB2 N N N 0 1.967 3.577 -5.608
113 HG13 H 3HG1 N N N 0 2.389 8.339 -6.811
114 HA4 H 4HA N N N 0 4.822 4.595 -6.209
115 HXT4 H 4HXT N N N 0 5.132 4.686 -2.811
116 H4 H 4H N N N 0 2.246 5.911 -6.593
117 HG23 H 3HG2 N N N 0 2.709 7.576 -8.371
118 HB13 H 3HB1 N N N 0 4.493 9.682 -7.077
119 HB23 H 3HB2 N N N 0 3.324 10.015 -8.343
120 HA3 H 3HA N N N 0 5.776 8.16 -8.65
121 HXT3 H 3HXT N N N 0 7.506 11.081 -9.008
122 H3 H 3H N N N 0 3.522 8.596 -10.451
123 HG12 H 2HG1 N N N 0 3.938 7.905 -12.756
124 HG22 H 2HG2 N N N 0 3.442 6.511 -11.791
125 HB12 H 2HB1 N N N 0 5.335 5.182 -12.603
126 HB22 H 2HB2 N N N 0 5.961 6.539 -13.524
127 HA2A H 2HA N N N 0 3.255 5.144 -14.056
128 HXT2 H 2HXT N N N 0 5.173 2.775 -15.594



KT5 : Chemical Bonds

Total Number of Bonds: 129
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N2A CD1 N C sing 1.39 N N
2 N2A CA2 N C sing 1.44 N N
3 N2A H2 N H sing 1.02 N N
4 CD1 OEB C O doub 1.23 N N
5 CD1 CG1 C C sing 1.52 N N
6 CG1 CB1 C C sing 1.53 N N
7 CG1 HG11 C H sing 1.1 N N
8 CG1 HG21 C H sing 1.1 N N
9 CB1 CA1 C C sing 1.53 N N
10 CB1 HB11 C H sing 1.1 N N
11 CB1 HB21 C H sing 1.1 N N
12 CA1 C1A C C sing 1.52 N N
13 CA1 N1A C N sing 1.44 N N
14 CA1 HA1A C H sing 1.09 N N
15 C1A O11 C O sing 1.36 N N
16 C1A O1A C O doub 1.22 N N
17 O11 HXT1 O H sing 0.98 N N
18 N1A C N C sing 1.39 N N
19 N1A H1 N H sing 1.02 N N
20 C O C O doub 1.23 N N
21 C C14 C C sing 1.48 N N
22 C14 C15 C C doub 1.38 N Y
23 C14 C13 C C sing 1.38 N Y
24 C15 C16 C C sing 1.4 N Y
25 C15 H15 C H sing 1.09 N N
26 C16 C11 C C doub 1.39 N Y
27 C16 H16 C H sing 1.09 N N
28 C13 C12 C C doub 1.39 N Y
29 C13 H13 C H sing 1.09 N N
30 C12 C11 C C sing 1.4 N Y
31 C12 H12 C H sing 1.09 N N
32 C11 C10 C C sing 1.49 N N
33 C10 C5 C C sing 1.57 N N
34 C10 C1 C C sing 1.57 N N
35 C10 H10 C H sing 1.11 N N
36 C5 C6 C C sing 1.53 N N
37 C5 OA2 C O sing 1.43 N N
38 C5 OA1 C O sing 1.43 N N
39 C6 F2 C F sing 1.35 N N
40 C6 F1 C F sing 1.35 N N
41 C6 F3 C F sing 1.35 N N
42 OA2 HA2 O H sing 0.97 N N
43 OA1 HA1 O H sing 0.97 N N
44 C1 C2 C C sing 1.54 N N
45 C1 H11 C H sing 1.1 N N
46 C1 H12A C H sing 1.1 N N
47 C2 C3 C C sing 1.53 N N
48 C2 H21 C H sing 1.1 N N
49 C2 H22 C H sing 1.1 N N
50 C3 C4 C C sing 1.51 N N
51 C3 H31 C H sing 1.1 N N
52 C3 H32 C H sing 1.1 N N
53 C4 C7 C C doub 1.37 N Y
54 C4 C9 C C sing 1.37 N Y
55 C7 N8 C N sing 1.42 N N
56 C7 N1 C N sing 1.35 N Y
57 N8 HN81 N H sing 1.0 N N
58 N8 HN82 N H sing 1.0 N N
59 C9 O1 C O sing 1.37 N N
60 C9 N3 C N doub 1.35 N Y
61 O1 HO1 O H sing 0.97 N N
62 N3 C8 N C sing 1.35 N Y
63 C8 N2 C N sing 1.41 N N
64 C8 N1 C N doub 1.35 N Y
65 N2 HN21 N H sing 1.0 N N
66 N2 HN22 N H sing 1.0 N N
67 OEF CD5 O C doub 1.22 N N
68 OEP CD5 O C sing 1.36 N N
69 OEP HE25 O H sing 0.98 N N
70 CD5 CG5 C C sing 1.51 N N
71 CG5 CB5 C C sing 1.53 N N
72 CG5 HG15 C H sing 1.09 N N
73 CG5 HG25 C H sing 1.1 N N
74 CB5 CA5 C C sing 1.54 N N
75 CB5 HB15 C H sing 1.1 N N
76 CB5 HB25 C H sing 1.1 N N
77 CA5 C5A C C sing 1.52 N N
78 CA5 N5 C N sing 1.44 N N
79 CA5 HA5 C H sing 1.1 N N
80 C5A O5 C O doub 1.22 N N
81 C5A O12 C O sing 1.36 N N
82 O12 HXT5 O H sing 0.98 N N
83 N5 CD4 N C sing 1.39 N N
84 N5 H5 N H sing 1.02 N N
85 OEE CD4 O C doub 1.23 N N
86 CD4 CG4 C C sing 1.52 N N
87 CG4 CB4 C C sing 1.53 N N
88 CG4 HG14 C H sing 1.1 N N
89 CG4 HG24 C H sing 1.1 N N
90 CB4 CA4 C C sing 1.53 N N
91 CB4 HB14 C H sing 1.1 N N
92 CB4 HB24 C H sing 1.1 N N
93 CA4 C4A C C sing 1.52 N N
94 CA4 N4 C N sing 1.44 N N
95 CA4 HA4 C H sing 1.09 N N
96 C4A O4 C O doub 1.22 N N
97 C4A O13 C O sing 1.36 N N
98 O13 HXT4 O H sing 0.98 N N
99 N4 CD3 N C sing 1.39 N N
100 N4 H4 N H sing 1.02 N N
101 OED CD3 O C doub 1.23 N N
102 CD3 CG3 C C sing 1.52 N N
103 CG3 CB3 C C sing 1.53 N N
104 CG3 HG13 C H sing 1.09 N N
105 CG3 HG23 C H sing 1.1 N N
106 CB3 CA3 C C sing 1.53 N N
107 CB3 HB13 C H sing 1.1 N N
108 CB3 HB23 C H sing 1.1 N N
109 CA3 C3A C C sing 1.52 N N
110 CA3 N3A C N sing 1.44 N N
111 CA3 HA3 C H sing 1.09 N N
112 C3A O3 C O doub 1.23 N N
113 C3A O14 C O sing 1.36 N N
114 O14 HXT3 O H sing 0.98 N N
115 N3A CD2 N C sing 1.39 N N
116 N3A H3 N H sing 1.02 N N
117 OEC CD2 O C doub 1.23 N N
118 CD2 CG2 C C sing 1.52 N N
119 CG2 CB2 C C sing 1.53 N N
120 CG2 HG12 C H sing 1.1 N N
121 CG2 HG22 C H sing 1.1 N N
122 CB2 CA2 C C sing 1.53 N N
123 CB2 HB12 C H sing 1.1 N N
124 CB2 HB22 C H sing 1.1 N N
125 CA2 C2A C C sing 1.52 N N
126 CA2 HA2A C H sing 1.09 N N
127 C2A O2 C O doub 1.22 N N
128 C2A O15 C O sing 1.36 N N
129 O15 HXT2 O H sing 0.98 N N



KT5 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
KT5 1rbm Open in New Window Bound ligand 2 1
KT5 1rbz Open in New Window Bound ligand 2 1
KT5 1rc0 Open in New Window Bound ligand 2 1