Chemical Components in the PDB

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RXT : Summary

Code

RXT

One-letter code

X

Molecule name

(3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile

Synonyms

Ruxolitinib

Systematic names

ProgramVersionName
ACDLabs 12.01 (3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile
OpenEye OEToolkits 1.9.2 (3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)pyrazol-1-yl]propanenitrile

Formula

C17 H18 N6

Formal charge

0

Molecular weight

306.365 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N#CCC(n1ncc(c1)c3ncnc2c3ccn2)C4CCCC4
SMILES CACTVS 3.385 N#CC[CH](C1CCCC1)n2cc(cn2)c3ncnc4[nH]ccc34
SMILES OpenEye OEToolkits 1.9.2 c1c[nH]c2c1c(ncn2)c3cnn(c3)C(CC#N)C4CCCC4
Canonical SMILES CACTVS 3.385 N#CC[C@H](C1CCCC1)n2cc(cn2)c3ncnc4[nH]ccc34
Canonical SMILES OpenEye OEToolkits 1.9.2 c1c[nH]c2c1c(ncn2)c3cnn(c3)[C@H](CC#N)C4CCCC4

IUPAC InChI

InChI=1S/C17H18N6/c18-7-5-15(12-3-1-2-4-12)23-10-13(9-22-23)16-14-6-8-19-17(14)21-11-20-16/h6,8-12,15H,1-5H2,(H,19,20,21)/t15-/m1/s1

IUPAC InChI key

HFNKQEVNSGCOJV-OAHLLOKOSA-N
RXT

wwPDB Information

Atom count

41 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-07-31

Last modified at

2014-09-12

Status

Released

Obsoleted

Not Assigned



RXT : 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 CAB C C8 N N N 0 -2.537 2.983 -0.425
2 CAC C C17 N Y N 0 4.499 -2.251 -0.638
3 CAD C C16 N Y N 0 3.243 -1.791 -0.77
4 CAE C C13 N Y N 0 3.745 1.717 1.309
5 CAF C C10 N Y N 0 0.468 -0.34 -1.594
6 CAG C C9 N Y N 0 -0.334 0.669 0.237
7 CAH C C2 N N N 0 -5.318 -1.911 1.063
8 CAI C C3 N N N 0 -4.243 -2.853 0.495
9 CAJ C C7 N N N 0 -2.948 1.875 0.453
10 CAK C C1 N N N 0 -4.857 -0.473 0.745
11 CAL C C4 N N N 0 -3.166 -1.956 -0.149
12 CAQ C C11 N Y N 0 0.823 0.279 -0.377
13 CAR C C12 N Y N 0 2.196 0.464 0.143
14 CAS C C15 N Y N 0 3.189 -0.504 -0.083
15 CAT C C14 N Y N 0 4.482 -0.277 0.43
16 CAU C C5 N N N 0 -3.322 -0.592 0.576
17 CAV C C6 R N N 0 -2.779 0.547 -0.288
18 H1 H H1 N N N 0 -5.316 -0.121 -0.179
19 H10 H H10 N N N 0 -3.329 0.584 -1.229
20 H11 H H11 N N N 0 -3.993 2.003 0.735
21 H12 H H12 N N N 0 -2.327 1.872 1.349
22 H18 H H18 N N N 0 -0.413 1.169 1.191
23 H19 H H19 N N N 0 1.153 -0.759 -2.316
24 H2 H H2 N N N 0 -5.1 0.197 1.569
25 H20 H H20 N N N 0 3.966 2.612 1.871
26 H21 H H21 N N N 0 2.43 -2.28 -1.286
27 H22 H H22 N N N 0 4.863 -3.185 -1.037
28 H23 H H23 N N N 0 6.188 -1.462 0.294
29 H3 H H3 N N N 0 -5.402 -2.046 2.141
30 H4 H H4 N N N 0 -6.279 -2.109 0.587
31 H5 H H5 N N N 0 -3.804 -3.446 1.298
32 H6 H H6 N N N 0 -4.681 -3.51 -0.257
33 H7 H H7 N N N 0 -2.172 -2.368 0.025
34 H8 H H8 N N N 0 -3.351 -1.843 -1.217
35 H9 H H9 N N N 0 -2.827 -0.612 1.547
36 NAA N N1 N N N 0 -2.22 3.838 -1.102
37 NAM N N4 N Y N 0 2.522 1.55 0.843
38 NAN N N6 N Y N 0 5.251 -1.35 0.07
39 NAO N N3 N Y N 0 -0.834 -0.31 -1.698
40 NAP N N5 N Y N 0 4.707 0.84 1.117
41 NAW N N2 N Y N 0 -1.359 0.318 -0.562



RXT : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAE NAM C N doub 1.32 N Y
2 CAE NAP C N sing 1.32 N Y
3 NAM CAR N C sing 1.33 N Y
4 NAP CAT N C doub 1.33 N Y
5 CAF CAQ C C sing 1.41 N Y
6 CAF NAO C N doub 1.31 N Y
7 CAR CAQ C C sing 1.48 N N
8 CAR CAS C C doub 1.41 N Y
9 CAQ CAG C C doub 1.37 N Y
10 NAO NAW N N sing 1.4 N Y
11 CAT CAS C C sing 1.41 N Y
12 CAT NAN C N sing 1.37 N Y
13 CAS CAD C C sing 1.46 N Y
14 NAN CAC N C sing 1.37 N Y
15 NAW CAG N C sing 1.35 N Y
16 NAW CAV N C sing 1.46 N N
17 CAJ CAB C C sing 1.47 N N
18 CAJ CAV C C sing 1.53 N N
19 CAD CAC C C doub 1.34 N Y
20 CAB NAA C N trip 1.14 N N
21 CAV CAU C C sing 1.53 N N
22 CAL CAI C C sing 1.54 N N
23 CAL CAU C C sing 1.55 N N
24 CAI CAH C C sing 1.54 N N
25 CAU CAK C C sing 1.55 N N
26 CAH CAK C C sing 1.54 N N
27 CAK H1 C H sing 1.09 N N
28 CAK H2 C H sing 1.09 N N
29 CAH H3 C H sing 1.09 N N
30 CAH H4 C H sing 1.09 N N
31 CAI H5 C H sing 1.09 N N
32 CAI H6 C H sing 1.09 N N
33 CAL H7 C H sing 1.09 N N
34 CAL H8 C H sing 1.09 N N
35 CAU H9 C H sing 1.09 N N
36 CAV H10 C H sing 1.09 N N
37 CAJ H11 C H sing 1.09 N N
38 CAJ H12 C H sing 1.09 N N
39 CAG H18 C H sing 1.08 N N
40 CAF H19 C H sing 1.08 N N
41 CAE H20 C H sing 1.08 N N
42 CAD H21 C H sing 1.08 N N
43 CAC H22 C H sing 1.08 N N
44 NAN H23 N H sing 0.97 N N



RXT : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
RXT 4u5j Open in New Window Bound ligand 2 1
RXT 6vgl Open in New Window Bound ligand 4 1