Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PLK : Summary

Code

PLK

One-letter code

X

Molecule name

(3R)-3-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-5-METHYLHEXANOIC ACID

Systematic names

ProgramVersionName
ACDLabs 12.01 (3R)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-5-methylhexanoic acid
OpenEye OEToolkits 1.7.2 (3R)-5-methyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]hexanoic acid

Formula

C15 H25 N2 O7 P

Formal charge

0

Molecular weight

376.342 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)CC(NCc1c(cnc(c1O)C)COP(=O)(O)O)CC(C)C
SMILES CACTVS 3.370 CC(C)C[CH](CC(O)=O)NCc1c(O)c(C)ncc1CO[P](O)(O)=O
SMILES OpenEye OEToolkits 1.7.2 Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CC(C)C)CC(=O)O)O
Canonical SMILES CACTVS 3.370 CC(C)C[C@H](CC(O)=O)NCc1c(O)c(C)ncc1CO[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.2 Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CC(C)C)CC(=O)O)O

IUPAC InChI

InChI=1S/C15H25N2O7P/c1-9(2)4-12(5-14(18)19)17-7-13-11(8-24-25(21,22)23)6-16-10(3)15(13)20/h6,9,12,17,20H,4-5,7-8H2,1-3H3,(H,18,19)(H2,21,22,23)/t12-/m1/s1

IUPAC InChI key

YMKBKDGGJWGJOL-GFCCVEGCSA-N
PLK

wwPDB Information

Atom count

50 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-05-30

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



PLK : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C11 C C11 N N N 0 0.681 -3.16 -2.066
2 C12 C C12 N N N 0 0.217 -2.984 -0.619
3 C16 C C16 N N N 0 3.59 -2.037 0.977
4 C13 C C13 N N N 0 -0.797 -4.076 -0.271
5 C14 C C14 N N N 0 1.421 -3.088 0.319
6 C15 C C15 R N N 0 2.357 -1.901 0.082
7 C17 C C17 N N N 0 4.568 -0.936 0.656
8 O11 O O11 N N N 0 5.73 -0.856 1.322
9 O12 O O12 N N N 0 4.305 -0.126 -0.201
10 N11 N N11 N N N 0 1.654 -0.652 0.403
11 C21 C C21 N N N 0 1.158 0.002 -0.815
12 C22 C C22 N Y N 0 0.579 1.348 -0.463
13 C23 C C23 N Y N 0 1.375 2.488 -0.462
14 O21 O O21 N N N 0 2.694 2.408 -0.78
15 C24 C C24 N Y N 0 0.804 3.708 -0.132
16 C25 C C25 N N N 0 1.655 4.953 -0.127
17 N21 N N21 N Y N 0 -0.475 3.791 0.176
18 C26 C C26 N Y N 0 -1.257 2.73 0.184
19 C27 C C27 N Y N 0 -0.761 1.48 -0.138
20 C28 C C28 N N N 0 -1.667 0.276 -0.131
21 O22 O O22 N N N 0 -2.99 0.676 0.234
22 P P P N N N 0 -4.22 -0.356 0.342
23 H131 H H131 N N N 0 -0.33 -5.054 -0.387
24 O1P O O1P N N N 0 -5.519 0.414 0.9
25 O2P O O2P N N N 0 -4.54 -0.965 -1.114
26 O3P O O3P N N N 0 -3.862 -1.454 1.268
27 H111 H H111 N N N 0 1.403 -2.382 -2.314
28 H112 H H112 N N N 0 1.147 -4.139 -2.181
29 H113 H H113 N N N 0 -0.177 -3.086 -2.734
30 H12 H H12 N N N 0 -0.25 -2.005 -0.504
31 H132 H H132 N N N 0 -1.127 -3.95 0.76
32 H133 H H133 N N N 0 -1.655 -4.002 -0.94
33 H141 H H141 N N N 0 1.077 -3.079 1.354
34 H142 H H142 N N N 0 1.956 -4.017 0.122
35 H15 H H15 N N N 0 2.666 -1.886 -0.963
36 H161 H H161 N N N 0 3.29 -1.964 2.022
37 H162 H H162 N N N 0 4.062 -3.004 0.801
38 H11 H H11 N N N 0 0.903 -0.817 1.056
39 HA H HA N N N 0 6.325 -0.132 1.081
40 H211 H H211 N N N 0 1.981 0.133 -1.518
41 H212 H H212 N N N 0 0.386 -0.618 -1.271
42 H253 H H253 N N N 0 2.682 4.69 0.127
43 H21 H H21 N N N 0 2.88 2.523 -1.722
44 H251 H H251 N N N 0 1.632 5.413 -1.115
45 H252 H H252 N N N 0 1.266 5.655 0.611
46 H26 H H26 N N N 0 -2.3 2.839 0.443
47 H281 H H281 N N N 0 -1.684 -0.172 -1.125
48 H282 H H282 N N N 0 -1.296 -0.453 0.589
49 H1P H H1P N N N 0 -6.3 -0.149 0.991
50 H2P H H2P N N N 0 -4.783 -0.3 -1.773



PLK : Chemical Bonds

Total Number of Bonds: 50
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C11 C12 C C sing 1.53 N N
2 C12 C13 C C sing 1.53 N N
3 C12 C14 C C sing 1.53 N N
4 C14 C15 C C sing 1.53 N N
5 C15 C16 C C sing 1.53 N N
6 C15 N11 C N sing 1.47 N N
7 C16 C17 C C sing 1.51 N N
8 C17 O11 C O sing 1.34 N N
9 C17 O12 C O doub 1.21 N N
10 N11 C21 N C sing 1.47 N N
11 C21 C22 C C sing 1.51 N N
12 C22 C23 C C sing 1.39 N Y
13 C22 C27 C C doub 1.39 N Y
14 C23 O21 C O sing 1.36 N N
15 C23 C24 C C doub 1.39 N Y
16 C24 C25 C C sing 1.51 N N
17 C24 N21 C N sing 1.32 N Y
18 N21 C26 N C doub 1.32 N Y
19 C26 C27 C C sing 1.38 N Y
20 C27 C28 C C sing 1.51 N N
21 C28 O22 C O sing 1.43 N N
22 O22 P O P sing 1.61 N N
23 P O1P P O sing 1.61 N N
24 P O2P P O sing 1.61 N N
25 P O3P P O doub 1.48 N N
26 C11 H111 C H sing 1.09 N N
27 C11 H112 C H sing 1.09 N N
28 C11 H113 C H sing 1.09 N N
29 C12 H12 C H sing 1.09 N N
30 C13 H131 C H sing 1.09 N N
31 C13 H132 C H sing 1.09 N N
32 C13 H133 C H sing 1.09 N N
33 C14 H141 C H sing 1.09 N N
34 C14 H142 C H sing 1.09 N N
35 C15 H15 C H sing 1.09 N N
36 C16 H161 C H sing 1.09 N N
37 C16 H162 C H sing 1.09 N N
38 N11 H11 N H sing 1.01 N N
39 O11 HA O H sing 0.97 N N
40 C21 H211 C H sing 1.09 N N
41 C21 H212 C H sing 1.09 N N
42 O21 H21 O H sing 0.97 N N
43 C25 H251 C H sing 1.09 N N
44 C25 H252 C H sing 1.09 N N
45 C25 H253 C H sing 1.09 N N
46 C26 H26 C H sing 1.08 N N
47 C28 H281 C H sing 1.09 N N
48 C28 H282 C H sing 1.09 N N
49 O1P H1P O H sing 0.97 N N
50 O2P H2P O H sing 0.97 N N



PLK : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
PLK 4ao4 Open in New Window Bound ligand 3 1