Chemical Components in the PDB

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K9L : Summary

Code

K9L

One-letter code

X

Molecule name

(1S,2S)-2-(3-fluorobenzyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}cyclopropanamine

Systematic names

ProgramVersionName
ACDLabs 12.01 (1S,2S)-2-(3-fluorobenzyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}cyclopropanamine
OpenEye OEToolkits 1.7.6 (1S,2S)-2-[(3-fluorophenyl)methyl]-N-[2-(2-imidazol-1-ylpyrimidin-4-yl)ethyl]cyclopropan-1-amine

Formula

C19 H20 F N5

Formal charge

0

Molecular weight

337.394 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Fc1cccc(c1)CC4CC4NCCc2nc(ncc2)n3ccnc3
SMILES CACTVS 3.385 Fc1cccc(C[CH]2C[CH]2NCCc3ccnc(n3)n4ccnc4)c1
SMILES OpenEye OEToolkits 1.7.6 c1cc(cc(c1)F)CC2CC2NCCc3ccnc(n3)n4ccnc4
Canonical SMILES CACTVS 3.385 Fc1cccc(C[C@H]2C[C@@H]2NCCc3ccnc(n3)n4ccnc4)c1
Canonical SMILES OpenEye OEToolkits 1.7.6 c1cc(cc(c1)F)C[C@H]2C[C@@H]2NCCc3ccnc(n3)n4ccnc4

IUPAC InChI

InChI=1S/C19H20FN5/c20-16-3-1-2-14(11-16)10-15-12-18(15)22-6-4-17-5-7-23-19(24-17)25-9-8-21-13-25/h1-3,5,7-9,11,13,15,18,22H,4,6,10,12H2/t15-,18-/m0/s1

IUPAC InChI key

CYEVFFVOLRMDHH-YJBOKZPZSA-N
K9L

wwPDB Information

Atom count

45 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-10-21

Last modified at

2014-12-19

Status

Released

Obsoleted

Not Assigned



K9L : Atoms of Molecule

Total Number of Atoms: 45
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N01 N N01 N Y N 0 6.351 -2.63 -0.339
2 C02 C C02 N Y N 0 5.365 -1.849 0.006
3 N03 N N03 N Y N 0 5.696 -0.568 -0.31
4 C04 C C04 N Y N 0 6.948 -0.604 -0.872
5 C05 C C05 N Y N 0 7.334 -1.893 -0.879
6 C1' C C1' N Y N 0 -5.173 -0.697 -0.497
7 N11 N N11 N Y N 0 3.719 0.434 0.455
8 C12 C C12 N Y N 0 4.912 0.567 -0.102
9 N13 N N13 N Y N 0 5.379 1.75 -0.467
10 C14 C C14 N Y N 0 4.662 2.846 -0.285
11 C15 C C15 N Y N 0 3.408 2.744 0.296
12 C16 C C16 N Y N 0 2.95 1.489 0.666
13 C17 C C17 N N N 0 1.592 1.329 1.301
14 C18 C C18 N N N 0 0.77 0.319 0.497
15 N19 N N19 N N N 0 -0.553 0.163 1.116
16 C2' C C2' N Y N 0 -5.677 0.557 -0.781
17 C21 C C21 S N N 0 -1.373 -0.801 0.37
18 C22 C C22 N N N 0 -2.173 -1.824 1.179
19 C23 C C23 S N N 0 -2.893 -0.669 0.478
20 C24 C C24 N N N 0 -3.722 -1.004 -0.764
21 C3' C C3' N Y N 0 -7.011 0.839 -0.536
22 C4' C C4' N Y N 0 -7.837 -0.138 -0.006
23 C5' C C5' N Y N 0 -7.33 -1.392 0.278
24 C6' C C6' N Y N 0 -5.998 -1.67 0.038
25 F7' F F7' N N N 0 -7.505 2.065 -0.814
26 H02 H H02 N N N 0 4.44 -2.166 0.465
27 H04 H H04 N N N 0 7.514 0.24 -1.237
28 H05 H H05 N N N 0 8.274 -2.27 -1.255
29 H14 H H14 N N N 0 5.049 3.809 -0.585
30 H15 H H15 N N N 0 2.801 3.623 0.457
31 H17 H H17 N N N 0 1.709 0.97 2.323
32 H17A H H17A N N N 0 1.08 2.291 1.309
33 H18 H H18 N N N 0 0.653 0.678 -0.525
34 H18A H H18A N N N 0 1.283 -0.642 0.489
35 HN19 H HN19 N N N 0 -0.47 -0.106 2.085
36 H2' H H2' N N N 0 -5.032 1.318 -1.195
37 H21 H H21 N N N 0 -0.962 -1.126 -0.586
38 H22 H H22 N N N 0 -2.29 -2.821 0.755
39 H22A H H22A N N N 0 -2.092 -1.781 2.265
40 H23 H H23 N N N 0 -3.285 0.133 1.104
41 H24 H H24 N N N 0 -3.612 -2.062 -1.0
42 H24A H H24A N N N 0 -3.373 -0.405 -1.605
43 H4' H H4' N N N 0 -8.877 0.081 0.186
44 H5' H H5' N N N 0 -7.975 -2.153 0.692
45 H6' H H6' N N N 0 -5.602 -2.65 0.26



K9L : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N01 C02 N C doub 1.3 N Y
2 N01 C05 N C sing 1.34 N Y
3 C02 N03 C N sing 1.36 N Y
4 N03 C04 N C sing 1.37 N Y
5 N03 C12 N C sing 1.4 N N
6 C04 C05 C C doub 1.35 N Y
7 C1' C2' C C doub 1.38 N Y
8 C1' C24 C C sing 1.51 N N
9 C1' C6' C C sing 1.38 N Y
10 N11 C12 N C doub 1.32 N Y
11 N11 C16 N C sing 1.32 N Y
12 C12 N13 C N sing 1.32 N Y
13 N13 C14 N C doub 1.32 N Y
14 C14 C15 C C sing 1.39 N Y
15 C15 C16 C C doub 1.39 N Y
16 C16 C17 C C sing 1.51 N N
17 C17 C18 C C sing 1.53 N N
18 C18 N19 C N sing 1.47 N N
19 N19 C21 N C sing 1.47 N N
20 C2' C3' C C sing 1.39 N Y
21 C21 C22 C C sing 1.53 N N
22 C21 C23 C C sing 1.53 N N
23 C22 C23 C C sing 1.53 N N
24 C23 C24 C C sing 1.53 N N
25 C3' C4' C C doub 1.38 N Y
26 C3' F7' C F sing 1.35 N N
27 C4' C5' C C sing 1.38 N Y
28 C5' C6' C C doub 1.38 N Y
29 C02 H02 C H sing 1.08 N N
30 C04 H04 C H sing 1.08 N N
31 C05 H05 C H sing 1.08 N N
32 C14 H14 C H sing 1.08 N N
33 C15 H15 C H sing 1.08 N N
34 C17 H17 C H sing 1.09 N N
35 C17 H17A C H sing 1.09 N N
36 C18 H18 C H sing 1.09 N N
37 C18 H18A C H sing 1.09 N N
38 N19 HN19 N H sing 1.01 N N
39 C2' H2' C H sing 1.08 N N
40 C21 H21 C H sing 1.09 N N
41 C22 H22 C H sing 1.09 N N
42 C22 H22A C H sing 1.09 N N
43 C23 H23 C H sing 1.09 N N
44 C24 H24 C H sing 1.09 N N
45 C24 H24A C H sing 1.09 N N
46 C4' H4' C H sing 1.08 N N
47 C5' H5' C H sing 1.08 N N
48 C6' H6' C H sing 1.08 N N



K9L : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
K9L 4d2z Open in New Window Bound ligand 2 1