Chemical Components in the PDB

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KXV : Summary

Code

KXV

One-letter code

X

Molecule name

{(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-methoxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}ac etic acid

Synonyms

CHROMOPHORE (CYS-TYR-GLY)-3-OMeY

Systematic names

ProgramVersionName
ACDLabs 12.01 {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-methoxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid
OpenEye OEToolkits 2.0.7 2-[(4~{Z})-2-[(1~{R})-1-azanyl-2-sulfanyl-ethyl]-4-[(3-methoxy-4-oxidanyl-phenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid

Formula

C15 H17 N3 O5 S

Formal charge

0

Molecular weight

351.378 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 NC(CS)C=1N(CC(=O)O)C(=O)C(N=1)=[C@H]c2ccc(c(c2)OC)O
SMILES CACTVS 3.385 COc1cc(ccc1O)C=C2N=C([CH](N)CS)N(CC(O)=O)C2=O
SMILES OpenEye OEToolkits 2.0.7 COc1cc(ccc1O)C=C2C(=O)N(C(=N2)C(CS)N)CC(=O)O
Canonical SMILES CACTVS 3.385 COc1cc(ccc1O)\C=C2/N=C([C@@H](N)CS)N(CC(O)=O)C2=O
Canonical SMILES OpenEye OEToolkits 2.0.7 COc1cc(ccc1O)/C=C\2/C(=O)N(C(=N2)[C@H](CS)N)CC(=O)O

IUPAC InChI

InChI=1S/C15H17N3O5S/c1-23-12-5-8(2-3-11(12)19)4-10-15(22)18(6-13(20)21)14(17-10)9(16)7-24/h2-5,9,19,24H,6-7,16H2,1H3,(H,20,21)/b10-4-/t9-/m0/s1

IUPAC InChI key

FYVOFWNKVHJCRZ-SGRPLGENSA-N
KXV

wwPDB Information

Atom count

41 (24 without Hydrogen)

Polymer type

Amino Acid

Type description

L-peptide linking

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2019-01-23

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



KXV : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C14 N N N 0 -4.14 -1.67 -0.634
2 C1 C C3 N N N 0 -1.658 0.091 0.646
3 C2 C C4 N N N 0 -1.082 -2.033 0.526
4 CA1 C C2 R N N 0 -2.525 1.319 0.76
5 CA2 C C5 N N N 0 0.106 -1.165 0.466
6 CA3 C C6 N N N 0 -3.54 -1.583 0.746
7 CB1 C C1 N N N 0 -2.836 1.856 -0.639
8 CB2 C C7 N N N 0 1.421 -1.561 0.348
9 CD1 C C9 N Y N 0 3.795 -0.961 -0.069
10 CD2 C C10 N Y N 0 2.169 0.807 0.268
11 CE1 C C11 N Y N 0 4.783 -0.011 -0.23
12 CE2 C C12 N Y N 0 3.163 1.746 0.111
13 CF C C15 N N N 0 6.314 -1.803 -0.555
14 CG2 C C8 N Y N 0 2.476 -0.559 0.182
15 CZ C C13 N Y N 0 4.469 1.345 -0.143
16 H1 H H16 N N N 0 5.566 2.566 -1.217
17 H2 H H18 N N N 0 6.045 -2.271 0.392
18 H3 H H19 N N N 0 5.716 -2.235 -1.357
19 H4 H H20 N N N 0 7.371 -1.973 -0.757
20 HA1 H H7 N N N 0 -3.456 1.06 1.265
21 HA31 H H9 N N N 0 -3.611 -2.555 1.234
22 HA32 H H10 N N N 0 -4.082 -0.841 1.332
23 HB11 H H5 N N N 0 -3.36 1.092 -1.213
24 HB12 H H6 N N N 0 -1.905 2.114 -1.144
25 HB2 H H11 N N N 0 1.673 -2.611 0.379
26 HD1 H H13 N N N 0 4.037 -2.012 -0.136
27 HD2 H H14 N N N 0 1.153 1.121 0.456
28 HE2 H H15 N N N 0 2.926 2.797 0.177
29 HG1 H H4 N N N 0 -4.069 3.69 -1.785
30 HN1 H H1 N N N 0 -1.658 2.042 2.481
31 HN2 H H2 N N Y 0 -0.951 2.605 1.086
32 HXT H HXT N N Y 0 -5.769 -2.058 -1.689
33 N N N1 N N N 0 -1.818 2.348 1.533
34 N2 N N2 N N N 0 -0.366 0.116 0.544
35 N3 N N3 N N N 0 -2.132 -1.19 0.642
36 O O O3 N N N 0 -3.462 -1.428 -1.604
37 O2 O O1 N N N 0 -1.112 -3.25 0.487
38 O4 O O4 N N N 0 6.063 -0.398 -0.479
39 OH O O2 N N N 0 5.444 2.277 -0.302
40 OXT O OXT N N Y 0 -5.429 -2.016 -0.785
41 SG1 S S1 N N N 0 -3.879 3.333 -0.502



KXV : Chemical Bonds

Total Number of Bonds: 42
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CF O4 C O sing 1.43 N N
2 O4 CE1 O C sing 1.36 N N
3 OH CZ O C sing 1.36 N N
4 CE1 CZ C C doub 1.39 N Y
5 CE1 CD1 C C sing 1.38 N Y
6 CZ CE2 C C sing 1.39 N Y
7 CD1 CG2 C C doub 1.4 N Y
8 CE2 CD2 C C doub 1.38 N Y
9 CG2 CD2 C C sing 1.4 N Y
10 CG2 CB2 C C sing 1.46 N N
11 CB2 CA2 C C doub 1.38 Z N
12 CA2 N2 C N sing 1.37 N N
13 CA2 C2 C C sing 1.47 N N
14 O2 C2 O C doub 1.22 N N
15 N2 C1 N C doub 1.3 N N
16 C2 N3 C N sing 1.35 N N
17 C1 N3 C N sing 1.37 N N
18 C1 CA1 C C sing 1.51 N N
19 N3 CA3 N C sing 1.47 N N
20 CB1 CA1 C C sing 1.53 N N
21 CB1 SG1 C S sing 1.81 N N
22 CA1 N C N sing 1.47 N N
23 C CA3 C C sing 1.51 N N
24 C O C O doub 1.21 N N
25 N HN1 N H sing 1.01 N N
26 N HN2 N H sing 1.01 N N
27 SG1 HG1 S H sing 1.35 N N
28 CB1 HB11 C H sing 1.09 N N
29 CB1 HB12 C H sing 1.09 N N
30 CA1 HA1 C H sing 1.09 N N
31 CA3 HA31 C H sing 1.09 N N
32 CA3 HA32 C H sing 1.09 N N
33 CB2 HB2 C H sing 1.08 N N
34 CD1 HD1 C H sing 1.08 N N
35 CD2 HD2 C H sing 1.08 N N
36 CE2 HE2 C H sing 1.08 N N
37 OH H1 O H sing 0.97 N N
38 C OXT C O sing 1.34 N N
39 CF H2 C H sing 1.09 N N
40 CF H3 C H sing 1.09 N N
41 CF H4 C H sing 1.09 N N
42 OXT HXT O H sing 0.97 N N



KXV : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
KXV 6nqs Open in New Window Polymer component 8 1