Chemical Components in the PDB

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5VP : Summary

Code

5VP

One-letter code

X

Molecule name

4-{[(2-chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)amino]methyl}phenol

Systematic names

ProgramVersionName
ACDLabs 12.01 4-{[(2-chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)amino]methyl}phenol
OpenEye OEToolkits 2.0.7 4-[[(2-chloranyl-5-phenyl-thieno[2,3-d]pyrimidin-4-yl)amino]methyl]phenol

Formula

C19 H14 Cl N3 O S

Formal charge

0

Molecular weight

367.852 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Oc1ccc(cc1)CNc1nc(Cl)nc2scc(c12)c1ccccc1
SMILES CACTVS 3.385 Oc1ccc(CNc2nc(Cl)nc3scc(c4ccccc4)c23)cc1
SMILES OpenEye OEToolkits 2.0.7 c1ccc(cc1)c2csc3c2c(nc(n3)Cl)NCc4ccc(cc4)O
Canonical SMILES CACTVS 3.385 Oc1ccc(CNc2nc(Cl)nc3scc(c4ccccc4)c23)cc1
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc(cc1)c2csc3c2c(nc(n3)Cl)NCc4ccc(cc4)O

IUPAC InChI

InChI=1S/C19H14ClN3OS/c20-19-22-17(21-10-12-6-8-14(24)9-7-12)16-15(11-25-18(16)23-19)13-4-2-1-3-5-13/h1-9,11,24H,10H2,(H,21,22,23)

IUPAC InChI key

NNBAZKOESMUGEL-UHFFFAOYSA-N
5VP

wwPDB Information

Atom count

39 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-07-23

Last modified at

2022-06-17

Status

Released

Obsoleted

Not Assigned



5VP : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 1.871 1.812 0.058
2 N3 N N2 N N N 0 -0.179 0.661 0.043
3 C4 C C1 N Y N 0 1.93 -0.549 -0.012
4 C5 C C2 N Y N 0 2.426 -2.84 -0.083
5 C6 C C3 N Y N 0 1.457 -1.927 -0.048
6 C7 C C4 N Y N 0 0.018 -2.283 -0.044
7 C8 C C5 N Y N 0 -0.824 -1.805 -1.047
8 C10 C C6 N Y N 0 -2.669 -2.948 -0.036
9 C13 C C7 N N N 0 -0.919 1.922 -0.043
10 C15 C C8 N Y N 0 -3.066 1.598 1.201
11 C17 C C9 N Y N 0 -5.116 1.123 0.052
12 C1 C C10 N Y N 0 1.204 0.668 0.031
13 C11 C C11 N Y N 0 -1.837 -3.431 0.958
14 C12 C C12 N Y N 0 -0.497 -3.102 0.96
15 C14 C C13 N Y N 0 -2.399 1.64 -0.009
16 C16 C C14 N Y N 0 -4.423 1.34 1.234
17 C18 C C15 N Y N 0 -4.444 1.165 -1.161
18 C19 C C16 N Y N 0 -3.087 1.424 -1.189
19 C2 C C17 N Y N 0 3.193 1.834 0.046
20 C3 C C18 N Y N 0 3.322 -0.472 -0.023
21 C9 C C19 N Y N 0 -2.162 -2.14 -1.038
22 N2 N N3 N Y N 0 3.908 0.733 0.007
23 O1 O O1 N N N 0 -6.45 0.868 0.082
24 S1 S S1 N Y N 0 4.01 -2.089 -0.078
25 CL1 CL CL1 N N N 0 4.009 3.365 0.083
26 H1 H H1 N N N 0 -0.659 -0.179 0.108
27 H2 H H2 N N N 0 2.258 -3.907 -0.113
28 H4 H H4 N N N 0 -0.429 -1.173 -1.829
29 H5 H H5 N N N 0 -3.718 -3.208 -0.034
30 H6 H H6 N N N 0 -0.651 2.559 0.801
31 H7 H H7 N N N 0 -0.666 2.429 -0.974
32 H8 H H8 N N N 0 -2.526 1.763 2.121
33 H9 H H9 N N N 0 -2.239 -4.062 1.738
34 H10 H H10 N N N 0 0.151 -3.48 1.737
35 H11 H H11 N N N 0 -4.944 1.307 2.18
36 H12 H H12 N N N 0 -4.981 0.997 -2.083
37 H13 H H13 N N N 0 -2.563 1.458 -2.133
38 H14 H H14 N N N 0 -2.816 -1.77 -1.814
39 H15 H H15 N N N 0 -7.003 1.66 0.029



5VP : 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 N1 C1 N C doub 1.32 N Y
2 N1 C2 N C sing 1.32 N Y
3 N3 C13 N C sing 1.46 N N
4 N3 C1 N C sing 1.38 N N
5 C4 C6 C C sing 1.46 N Y
6 C4 C1 C C sing 1.42 N Y
7 C4 C3 C C doub 1.39 N Y
8 C5 C6 C C doub 1.33 N Y
9 C5 S1 C S sing 1.75 N Y
10 C6 C7 C C sing 1.48 N N
11 C7 C8 C C doub 1.39 N Y
12 C7 C12 C C sing 1.39 N Y
13 C8 C9 C C sing 1.38 N Y
14 C10 C11 C C sing 1.38 N Y
15 C10 C9 C C doub 1.38 N Y
16 C13 C14 C C sing 1.51 N N
17 C15 C14 C C doub 1.38 N Y
18 C15 C16 C C sing 1.38 N Y
19 C17 C16 C C doub 1.39 N Y
20 C17 C18 C C sing 1.39 N Y
21 C17 O1 C O sing 1.36 N N
22 C11 C12 C C doub 1.38 N Y
23 C14 C19 C C sing 1.38 N Y
24 C18 C19 C C doub 1.38 N Y
25 C2 N2 C N doub 1.31 N Y
26 C2 CL1 C CL sing 1.74 N N
27 C3 N2 C N sing 1.34 N Y
28 C3 S1 C S sing 1.76 N Y
29 N3 H1 N H sing 0.97 N N
30 C5 H2 C H sing 1.08 N N
31 C8 H4 C H sing 1.08 N N
32 C10 H5 C H sing 1.08 N N
33 C13 H6 C H sing 1.09 N N
34 C13 H7 C H sing 1.09 N N
35 C15 H8 C H sing 1.08 N N
36 C11 H9 C H sing 1.08 N N
37 C12 H10 C H sing 1.08 N N
38 C16 H11 C H sing 1.08 N N
39 C18 H12 C H sing 1.08 N N
40 C19 H13 C H sing 1.08 N N
41 C9 H14 C H sing 1.08 N N
42 O1 H15 O H sing 0.97 N N



5VP : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5VP 7rke Open in New Window Bound ligand 2 1