Chemical Components in the PDB

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5R4 : Summary

Code

5R4

One-letter code

X

Molecule name

3-[3-(acetyl{[(1R,2R,3S,4R)-4-(4-chloro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,3-dihydroxycyclopentyl]methyl}amino)prop-1-yn-1-yl]benzamide

Systematic names

ProgramVersionName
ACDLabs 12.01 3-[3-(acetyl{[(1R,2R,3S,4R)-4-(4-chloro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,3-dihydroxycyclopentyl]methyl}amino)prop-1-yn-1-yl]benzamide
OpenEye OEToolkits 2.0.7 3-[3-[[(1~{R},2~{R},3~{S},4~{R})-4-(4-chloranylpyrrolo[2,3-d]pyrimidin-7-yl)-2,3-bis(oxidanyl)cyclopentyl]methyl-ethanoyl-amino]prop-1-ynyl]benzamide

Formula

C24 H24 Cl N5 O4

Formal charge

0

Molecular weight

481.931 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 NC(=O)c1cccc(c1)C#CCN(CC1CC(C(O)C1O)n1ccc2c1ncnc2Cl)C(C)=O
SMILES CACTVS 3.385 CC(=O)N(CC#Cc1cccc(c1)C(N)=O)C[CH]2C[CH]([CH](O)[CH]2O)n3ccc4c(Cl)ncnc34
SMILES OpenEye OEToolkits 2.0.7 CC(=O)N(CC#Cc1cccc(c1)C(=O)N)CC2CC(C(C2O)O)n3ccc4c3ncnc4Cl
Canonical SMILES CACTVS 3.385 CC(=O)N(CC#Cc1cccc(c1)C(N)=O)C[C@H]2C[C@H]([C@H](O)[C@@H]2O)n3ccc4c(Cl)ncnc34
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(=O)N(CC#Cc1cccc(c1)C(=O)N)C[C@H]2C[C@H]([C@@H]([C@@H]2O)O)n3ccc4c3ncnc4Cl

IUPAC InChI

InChI=1S/C24H24ClN5O4/c1-14(31)29(8-3-5-15-4-2-6-16(10-15)23(26)34)12-17-11-19(21(33)20(17)32)30-9-7-18-22(25)27-13-28-24(18)30/h2,4,6-7,9-10,13,17,19-21,32-33H,8,11-12H2,1H3,(H2,26,34)/t17-,19-,20-,21+/m1/s1

IUPAC InChI key

AHVJTPYPUIHNLS-WLRLJWMZSA-N
5R4

wwPDB Information

Atom count

58 (34 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

2022-07-15

Status

Released

Obsoleted

Not Assigned



5R4 : Atoms of Molecule

Total Number of Atoms: 58
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N15 N N1 N N N 0 -1.568 -1.494 0.187
2 C23 C C1 N Y N 0 -5.991 0.986 1.618
3 C24 C C2 N Y N 0 -7.129 1.648 2.035
4 C30 C C3 N Y N 0 -6.95 0.709 -0.579
5 C26 C C7 N Y N 0 -8.099 1.369 -0.15
6 C31 C C4 R N N 0 1.315 -2.189 -0.072
7 C33 C C5 S N N 0 2.779 -1.848 0.278
8 C27 C C6 N N N 0 -9.225 1.582 -1.086
9 C25 C C8 N Y N 0 -8.181 1.842 1.162
10 C14 C C9 N N N 0 -0.503 -0.496 0.312
11 C17 C C10 N N N 0 -2.821 -3.457 1.021
12 C22 C C11 N Y N 0 -5.895 0.512 0.309
13 C21 C C12 N N N 0 -4.709 -0.165 -0.124
14 C19 C C13 N N N 0 -2.519 -1.416 -0.924
15 C12 C C14 N N N 0 1.766 0.197 -0.529
16 C02 C C15 N Y N 0 7.407 1.658 -0.108
17 C04 C C16 N Y N 0 7.078 0.628 -2.142
18 C06 C C17 N Y N 0 5.369 0.469 -0.616
19 C07 C C18 N Y N 0 6.141 1.226 0.289
20 C08 C C19 N Y N 0 5.331 1.361 1.5
21 C09 C C20 N Y N 0 4.178 0.713 1.27
22 C11 C C21 R N N 0 3.094 -0.599 -0.582
23 C13 C C22 R N N 0 0.672 -0.889 -0.586
24 C16 C C23 N N N 0 -1.669 -2.488 1.092
25 C20 C C24 N N N 0 -3.738 -0.72 -0.479
26 N03 N N2 N Y N 0 7.83 1.339 -1.321
27 N05 N N3 N Y N 0 5.879 0.198 -1.813
28 N10 N N4 N Y N 0 4.188 0.176 0.009
29 N28 N N5 N N N 0 -10.336 2.22 -0.669
30 O18 O O1 N N N 0 -0.834 -2.602 1.964
31 O29 O O2 N N N 0 -9.147 1.181 -2.23
32 O32 O O3 N N N 0 1.277 -3.19 -1.091
33 O34 O O4 N N N 0 3.643 -2.93 -0.074
34 H3 H H3 N N N 0 -6.882 0.341 -1.592
35 H4 H H4 N N N 0 0.79 -2.54 0.816
36 H5 H H5 N N N 0 2.872 -1.614 1.339
37 H6 H H6 N N N 0 -9.068 2.361 1.493
38 H7 H H7 N N N 0 -0.882 0.48 0.008
39 H8 H H8 N N N 0 -0.169 -0.449 1.348
40 H9 H H9 N N N 0 -3.453 -3.209 0.168
41 H10 H H10 N N N 0 -2.437 -4.47 0.906
42 H11 H H11 N N N 0 -3.407 -3.393 1.938
43 H12 H H12 N N N 0 -2.068 -0.866 -1.75
44 H13 H H13 N N N 0 -2.776 -2.422 -1.254
45 H14 H H14 N N N 0 1.696 0.761 0.401
46 H15 H H15 N N N 0 1.686 0.865 -1.386
47 H16 H H16 N N N 0 7.463 0.391 -3.123
48 H17 H H17 N N N 0 5.608 1.881 2.405
49 H18 H H18 N N N 0 3.364 0.627 1.974
50 H19 H H19 N N N 0 3.332 -0.886 -1.606
51 H20 H H20 N N N 0 0.33 -1.022 -1.612
52 H21 H H21 N N N 0 -11.074 2.36 -1.282
53 H22 H H22 N N N 0 -10.398 2.54 0.245
54 H23 H H23 N N N 0 1.668 -4.034 -0.828
55 H24 H H24 N N N 0 3.489 -3.738 0.434
56 H2 H H2 N N N 0 -7.197 2.016 3.048
57 CL1 CL CL1 N N N 0 8.4 2.599 0.961
58 H1 H H1 N N N 0 -5.172 0.838 2.307



5R4 : Chemical Bonds

Total Number of Bonds: 61
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CL1 C02 CL C sing 1.74 N N
2 C08 C09 C C doub 1.34 N Y
3 C08 C07 C C sing 1.46 N Y
4 C09 N10 C N sing 1.37 N Y
5 C02 C07 C C doub 1.4 N Y
6 C02 N03 C N sing 1.32 N Y
7 C07 C06 C C sing 1.41 N Y
8 N03 C04 N C doub 1.32 N Y
9 N10 C06 N C sing 1.37 N Y
10 N10 C11 N C sing 1.47 N N
11 C06 N05 C N doub 1.33 N Y
12 C33 C11 C C sing 1.55 N N
13 C33 O34 C O sing 1.43 N N
14 C33 C31 C C sing 1.54 N N
15 C04 N05 C N sing 1.32 N Y
16 C11 C12 C C sing 1.55 N N
17 C12 C13 C C sing 1.54 N N
18 N28 C27 N C sing 1.35 N N
19 C31 C13 C C sing 1.54 N N
20 C31 O32 C O sing 1.43 N N
21 C13 C14 C C sing 1.53 N N
22 C27 O29 C O doub 1.21 N N
23 C27 C26 C C sing 1.48 N N
24 C14 N15 C N sing 1.46 N N
25 C30 C26 C C doub 1.39 N Y
26 C30 C22 C C sing 1.39 N Y
27 C26 C25 C C sing 1.4 N Y
28 C19 C20 C C sing 1.47 N N
29 C19 N15 C N sing 1.46 N N
30 C20 C21 C C trip 1.17 N N
31 C21 C22 C C sing 1.43 N N
32 C22 C23 C C doub 1.4 N Y
33 N15 C16 N C sing 1.35 N N
34 C25 C24 C C doub 1.38 N Y
35 C23 C24 C C sing 1.38 N Y
36 C16 C17 C C sing 1.51 N N
37 C16 O18 C O doub 1.21 N N
38 C23 H1 C H sing 1.08 N N
39 C24 H2 C H sing 1.08 N N
40 C30 H3 C H sing 1.08 N N
41 C31 H4 C H sing 1.09 N N
42 C33 H5 C H sing 1.09 N N
43 C25 H6 C H sing 1.08 N N
44 C14 H7 C H sing 1.09 N N
45 C14 H8 C H sing 1.09 N N
46 C17 H9 C H sing 1.09 N N
47 C17 H10 C H sing 1.09 N N
48 C17 H11 C H sing 1.09 N N
49 C19 H12 C H sing 1.09 N N
50 C19 H13 C H sing 1.09 N N
51 C12 H14 C H sing 1.09 N N
52 C12 H15 C H sing 1.09 N N
53 C04 H16 C H sing 1.08 N N
54 C08 H17 C H sing 1.08 N N
55 C09 H18 C H sing 1.08 N N
56 C11 H19 C H sing 1.09 N N
57 C13 H20 C H sing 1.09 N N
58 N28 H21 N H sing 0.97 N N
59 N28 H22 N H sing 0.97 N N
60 O32 H23 O H sing 0.97 N N
61 O34 H24 O H sing 0.97 N N



5R4 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
5R4 7rkk Open in New Window Bound ligand 2 1
5R4 7rkl Open in New Window Bound ligand 4 1