Chemical Components in the PDB

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KFP : Summary

Code

KFP

One-letter code

K

Molecule name

N~6~-[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]-D-lysine

Systematic names

ProgramVersionName
ACDLabs 12.01 N~6~-[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]-D-lysine
OpenEye OEToolkits 1.7.6 (2R)-2-azanyl-6-[(2-azanyl-4-oxidanylidene-3H-pteridin-6-yl)methylamino]hexanoic acid

Formula

C13 H19 N7 O3

Formal charge

0

Molecular weight

321.335 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(N)CCCCNCc2nc1c(N=C(N)NC1=O)nc2
SMILES CACTVS 3.370 N[CH](CCCCNCc1cnc2N=C(N)NC(=O)c2n1)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 c1c(nc2c(n1)N=C(NC2=O)N)CNCCCCC(C(=O)O)N
Canonical SMILES CACTVS 3.370 N[C@H](CCCCNCc1cnc2N=C(N)NC(=O)c2n1)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 c1c(nc2c(n1)N=C(NC2=O)N)CNCCCC[C@H](C(=O)O)N

IUPAC InChI

InChI=1S/C13H19N7O3/c14-8(12(22)23)3-1-2-4-16-5-7-6-17-10-9(18-7)11(21)20-13(15)19-10/h6,8,16H,1-5,14H2,(H,22,23)(H3,15,17,19,20,21)/t8-/m1/s1

IUPAC InChI key

VSWOPALBOJUOOW-MRVPVSSYSA-N
KFP

wwPDB Information

Atom count

42 (23 without Hydrogen)

Polymer type

Amino Acid

Type description

D-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

LYS

Defined at

2013-03-25

Last modified at

2013-04-19

Status

Released

Obsoleted

Not Assigned



KFP : Atoms of Molecule

Total Number of Atoms: 42
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 7.563 0.857 -0.529
2 C2 C C2 N N N 0 -6.345 0.557 -0.781
3 C4 C C4 N N N 0 -4.659 1.433 0.615
4 C4A C C4A N Y N 0 -3.884 0.211 0.342
5 C6 C C6 N Y N 0 -2.028 -1.099 0.597
6 C7 C C7 N Y N 0 -2.582 -2.058 -0.246
7 C8A C C8A N Y N 0 -4.455 -0.762 -0.512
8 CA C CA R N N 0 6.561 0.076 0.282
9 CAF C CAF N N N 0 -0.665 -1.329 1.196
10 CAH C CAH N N N 0 2.729 -0.191 0.021
11 CAI C CAI N N N 0 4.13 -0.403 0.599
12 CAJ C CAJ N N N 0 1.698 -0.881 0.916
13 CB C CB N N N 0 5.161 0.288 -0.296
14 H10 H H10 N N N 0 2.513 0.877 -0.026
15 H11 H H11 N N N 0 2.682 -0.615 -0.982
16 H12 H H12 N N N 0 1.914 -1.949 0.963
17 H13 H H13 N N N 0 1.745 -0.457 1.919
18 H14 H H14 N N N 0 0.302 -1.005 -0.592
19 H16 H H16 N N N 0 -0.465 -2.399 1.245
20 H17 H H17 N N N 0 -0.634 -0.907 2.201
21 H18 H H18 N N N 0 -6.411 2.338 0.186
22 H19 H H19 N N N 0 -8.097 1.516 -1.179
23 H2 H H2 N N N 0 6.583 0.421 1.316
24 H20 H H20 N N N 0 -7.937 0.024 -1.934
25 H21 H H21 N N N 0 -2.03 -2.96 -0.464
26 H3 H H3 N N N 0 6.281 -1.89 0.822
27 H4 H H4 N N Y 0 6.886 -1.696 -0.715
28 H6 H H6 N N N 0 4.944 1.355 -0.343
29 H7 H H7 N N N 0 5.113 -0.137 -1.299
30 H8 H H8 N N N 0 4.346 -1.47 0.646
31 H9 H H9 N N N 0 4.177 0.022 1.602
32 HXT H HXT N N Y 0 8.374 2.631 -0.86
33 N N N N N N 0 6.9 -1.352 0.234
34 N1 N N1 N N N 0 -5.673 -0.539 -1.038
35 N2 N N2 N N N 0 -7.58 0.714 -1.354
36 N3 N N3 N N N 0 -5.873 1.547 0.029
37 N5 N N5 N Y N 0 -2.684 0.011 0.871
38 N8 N N8 N Y N 0 -3.776 -1.879 -0.777
39 NAL N NAL N N N 0 0.353 -0.678 0.361
40 O O O N N N 0 8.231 0.297 -1.366
41 O4 O O4 N N N 0 -4.223 2.308 1.339
42 OXT O OXT N N Y 0 7.717 2.174 -0.318



KFP : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N CA N C sing 1.47 N N
2 CA CB C C sing 1.53 N N
3 CA C C C sing 1.51 N N
4 CB CAI C C sing 1.53 N N
5 O4 C4 O C doub 1.22 N N
6 C O C O doub 1.21 N N
7 C4 N3 C N sing 1.35 N N
8 C4 C4A C C sing 1.47 N N
9 CAI CAH C C sing 1.53 N N
10 N3 C2 N C sing 1.36 N N
11 CAH CAJ C C sing 1.53 N N
12 N5 C4A N C doub 1.33 N Y
13 N5 C6 N C sing 1.32 N Y
14 C4A C8A C C sing 1.41 N Y
15 C2 N2 C N sing 1.37 N N
16 C2 N1 C N doub 1.31 N N
17 CAF C6 C C sing 1.51 N N
18 CAF NAL C N sing 1.47 N N
19 C6 C7 C C doub 1.39 N Y
20 C8A N1 C N sing 1.35 N N
21 C8A N8 C N doub 1.33 N Y
22 NAL CAJ N C sing 1.47 N N
23 C7 N8 C N sing 1.32 N Y
24 CA H2 C H sing 1.09 N N
25 N H3 N H sing 1.01 N N
26 N H4 N H sing 1.01 N N
27 CB H6 C H sing 1.09 N N
28 CB H7 C H sing 1.09 N N
29 CAI H8 C H sing 1.09 N N
30 CAI H9 C H sing 1.09 N N
31 CAH H10 C H sing 1.09 N N
32 CAH H11 C H sing 1.09 N N
33 CAJ H12 C H sing 1.09 N N
34 CAJ H13 C H sing 1.09 N N
35 NAL H14 N H sing 1.01 N N
36 CAF H16 C H sing 1.09 N N
37 CAF H17 C H sing 1.09 N N
38 N3 H18 N H sing 0.97 N N
39 N2 H19 N H sing 0.97 N N
40 N2 H20 N H sing 0.97 N N
41 C7 H21 C H sing 1.08 N N
42 C OXT C O sing 1.34 N N
43 OXT HXT O H sing 0.97 N N



KFP : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
KFP 4iiq Open in New Window Polymer component 1 1
KFP 4l8s Open in New Window Polymer component 1 1
KFP 4l9l Open in New Window Polymer component 1 1