Chemical Components in the PDB

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K7K : Summary

Code

K7K

One-letter code

S

Molecule name

2-azanyl-3-[hexyl-[2-(3-oxidanylpyridin-2-yl)pyridin-3-yl]oxy-phosphoryl]oxy-propanal

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (2~{S})-2-azanyl-3-[hexyl-[2-(3-oxidanylpyridin-2-yl)pyridin-3-yl]oxy-phosphoryl]oxy-propanoic acid

Formula

C19 H26 N3 O6 P

Formal charge

0

Molecular weight

423.4 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCCCCC[P](=O)(OC[CH](N)C(O)=O)Oc1cccnc1c2ncccc2O
SMILES OpenEye OEToolkits 2.0.7 CCCCCCP(=O)(OCC(C(=O)O)N)Oc1cccnc1c2c(cccn2)O
Canonical SMILES CACTVS 3.385 CCCCCC[P@](=O)(OC[C@H](N)C(O)=O)Oc1cccnc1c2ncccc2O
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCCCC[P@](=O)(OC[C@@H](C(=O)O)N)Oc1cccnc1c2c(cccn2)O

IUPAC InChI

InChI=1S/C19H26N3O6P/c1-2-3-4-5-12-29(26,27-13-14(20)19(24)25)28-16-9-7-11-22-18(16)17-15(23)8-6-10-21-17/h6-11,14,23H,2-5,12-13,20H2,1H3,(H,24,25)/t14-,29-/m0/s1

IUPAC InChI key

XBHSCEFLQPYSRV-MMEWPQADSA-N
K7K

wwPDB Information

Atom count

55 (29 without Hydrogen)

Polymer type

Amino Acid

Type description

L-peptide linking

Type code

ATOMP

Is modified

Yes

Standard parent

SER

Defined at

2019-05-01

Last modified at

2021-06-22

Status

Released

Obsoleted

Not Assigned



K7K : Atoms of Molecule

Total Number of Atoms: 55
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N1 N N N 0 -1.079 2.672 0.525
2 C10 C C1 N Y N 0 -3.496 -2.153 -1.695
3 C11 C C2 N Y N 0 -2.411 -2.847 -2.2
4 C12 C C3 N Y N 0 -1.198 -2.796 -1.529
5 C13 C C4 N Y N 0 -2.189 -0.562 1.328
6 C14 C C5 N Y N 0 -3.328 0.113 1.779
7 C15 C C6 N Y N 0 -3.246 0.866 2.944
8 C16 C C7 N Y N 0 -2.034 0.917 3.615
9 C17 C C8 N Y N 0 -0.948 0.223 3.11
10 CA C C9 S N N 0 -0.742 2.428 -0.884
11 C C C10 N N N 0 -1.872 2.902 -1.76
12 O O O1 N N N 0 -2.977 3.05 -1.294
13 CB C C11 N N N 0 -0.519 0.93 -1.103
14 OG O O2 N N N 0 0.626 0.506 -0.361
15 P01 P P1 S N N 0 1.155 -1.015 -0.358
16 C01 C C12 N N N 0 2.712 -1.116 0.584
17 C02 C C14 N N N 0 3.796 -0.312 -0.137
18 C07 C C13 N Y N 0 -1.117 -2.044 -0.364
19 N01 N N2 N Y N 0 -3.395 -1.447 -0.588
20 O01 O O3 N N N 0 1.391 -1.458 -1.751
21 C08 C C15 N Y N 0 -2.256 -1.369 0.087
22 N02 N N3 N Y N 0 -1.048 -0.48 2.0
23 O02 O O4 N N N 0 -4.495 0.035 1.089
24 C03 C C16 N N N 0 5.103 -0.396 0.654
25 O03 O O5 N N N 0 0.051 -1.966 0.327
26 C04 C C17 N N N 0 6.188 0.408 -0.066
27 C05 C C18 N N N 0 7.495 0.324 0.725
28 C06 C C19 N N N 0 8.579 1.128 0.005
29 H1 H H1 N N N 0 -1.168 3.66 0.71
30 H2 H H2 N N N 0 -1.92 2.178 0.786
31 H4 H H4 N N N 0 -4.439 -2.188 -2.219
32 H5 H H5 N N N 0 -2.507 -3.423 -3.108
33 H6 H H6 N N N 0 -0.337 -3.33 -1.904
34 H7 H H7 N N N 0 -4.108 1.399 3.319
35 H14 H H14 N N N 0 2.56 -0.707 1.582
36 H8 H H8 N N N 0 -1.938 1.493 4.523
37 H9 H H9 N N N 0 -0.003 0.262 3.631
38 H10 H H10 N N N 0 0.168 2.972 -1.138
39 H12 H H12 N N N 0 -1.396 0.379 -0.765
40 H13 H H13 N N N 0 -0.356 0.739 -2.163
41 H15 H H15 N N N 0 3.023 -2.158 0.661
42 H16 H H16 N N N 0 3.949 -0.72 -1.135
43 H17 H H17 N N N 0 3.485 0.73 -0.214
44 H18 H H18 N N N 0 -5.065 -0.697 1.362
45 H19 H H19 N N N 0 4.951 0.013 1.653
46 H20 H H20 N N N 0 5.415 -1.438 0.731
47 H21 H H21 N N N 0 6.34 0.0 -1.065
48 H22 H H22 N N N 0 5.877 1.45 -0.143
49 H23 H H23 N N N 0 7.343 0.732 1.724
50 H24 H H24 N N N 0 7.806 -0.718 0.802
51 H25 H H25 N N N 0 8.732 0.719 -0.994
52 H26 H H26 N N N 0 8.268 2.17 -0.073
53 H27 H H27 N N N 0 9.511 1.068 0.568
54 OXT O OXT N N Y 0 -1.652 3.159 -3.059
55 HXT H HXT N N Y 0 -2.408 3.46 -3.582



K7K : Chemical Bonds

Total Number of Bonds: 56
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C10 C11 C C doub 1.38 N Y
2 C10 N01 C N sing 1.32 N Y
3 C11 C12 C C sing 1.39 N Y
4 N01 C08 N C doub 1.33 N Y
5 C12 C07 C C doub 1.39 N Y
6 N02 C17 N C doub 1.32 N Y
7 N02 C13 N C sing 1.33 N Y
8 C08 C07 C C sing 1.4 N Y
9 C08 C13 C C sing 1.48 N N
10 C17 C16 C C sing 1.38 N Y
11 C07 O03 C O sing 1.36 N N
12 C13 C14 C C doub 1.4 N Y
13 N CA N C sing 1.47 N N
14 C16 C15 C C doub 1.39 N Y
15 O03 P01 O P sing 1.61 N N
16 C14 C15 C C sing 1.39 N Y
17 C14 O02 C O sing 1.36 N N
18 OG P01 O P sing 1.61 N N
19 OG CB O C sing 1.43 N N
20 O01 P01 O P doub 1.48 N N
21 P01 C01 P C sing 1.82 N N
22 CA C C C sing 1.51 N N
23 CA CB C C sing 1.53 N N
24 C O C O doub 1.21 N N
25 C01 C02 C C sing 1.53 N N
26 C02 C03 C C sing 1.53 N N
27 C03 C04 C C sing 1.53 N N
28 C05 C04 C C sing 1.53 N N
29 C05 C06 C C sing 1.53 N N
30 N H1 N H sing 1.01 N N
31 N H2 N H sing 1.01 N N
32 C10 H4 C H sing 1.08 N N
33 C11 H5 C H sing 1.08 N N
34 C12 H6 C H sing 1.08 N N
35 C15 H7 C H sing 1.08 N N
36 C16 H8 C H sing 1.08 N N
37 C17 H9 C H sing 1.08 N N
38 CA H10 C H sing 1.09 N N
39 CB H12 C H sing 1.09 N N
40 CB H13 C H sing 1.09 N N
41 C01 H14 C H sing 1.09 N N
42 C01 H15 C H sing 1.09 N N
43 C02 H16 C H sing 1.09 N N
44 C02 H17 C H sing 1.09 N N
45 O02 H18 O H sing 0.97 N N
46 C03 H19 C H sing 1.09 N N
47 C03 H20 C H sing 1.09 N N
48 C04 H21 C H sing 1.09 N N
49 C04 H22 C H sing 1.09 N N
50 C05 H23 C H sing 1.09 N N
51 C05 H24 C H sing 1.09 N N
52 C06 H25 C H sing 1.09 N N
53 C06 H26 C H sing 1.09 N N
54 C06 H27 C H sing 1.09 N N
55 OXT HXT O H sing 0.97 N N
56 C OXT C O sing 1.34 N N



K7K : Used in PDB Entries

Total Number of PDB Entries: 0
Ligand Code PDB Entry ID Type Total Distinct