Chemical Components in the PDB

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IP1 : Summary

Code

IP1

One-letter code

X

Molecule name

ISOPENICILLIN N

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S,5R,6R)-6-{[(5S)-5-amino-5-carboxypentanoyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
OpenEye OEToolkits 1.5.0 (2S,5R,6R)-6-[[(5S)-5-amino-6-hydroxy-6-oxo-hexanoyl]amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

Formula

C14 H21 N3 O6 S

Formal charge

0

Molecular weight

359.398 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C1N2C(=O)C(NC(=O)CCCC(C(=O)O)N)C2SC1(C)C
SMILES CACTVS 3.341 CC1(C)S[CH]2[CH](NC(=O)CCC[CH](N)C(O)=O)C(=O)N2[CH]1C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC1(C(N2C(S1)C(C2=O)NC(=O)CCCC(C(=O)O)N)C(=O)O)C
Canonical SMILES CACTVS 3.341 CC1(C)S[C@@H]2[C@H](NC(=O)CCC[C@H](N)C(O)=O)C(=O)N2[C@H]1C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)CCC[C@@H](C(=O)O)N)C(=O)O)C

IUPAC InChI

InChI=1S/C14H21N3O6S/c1-14(2)9(13(22)23)17-10(19)8(11(17)24-14)16-7(18)5-3-4-6(15)12(20)21/h6,8-9,11H,3-5,15H2,1-2H3,(H,16,18)(H,20,21)(H,22,23)/t6-,8+,9-,11+/m0/s1

IUPAC InChI key

MIFYHUACUWQUKT-GTQWGBSQSA-N
IP1

wwPDB Information

Atom count

45 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



IP1 : 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 C1 C C1 N N N 0 0.658 0.642 -7.094
2 C2 C C2 S N N 0 -0.289 0.205 -6.007
3 C3 C C3 N N N 0 0.409 0.309 -4.649
4 C4 C C4 N N N 0 -0.552 -0.134 -3.545
5 C7 C C7 N N N 0 0.146 -0.03 -2.188
6 C10 C C10 N N N 0 -0.801 -0.467 -1.101
7 N11 N N11 N N N 0 -0.4 -0.459 0.185
8 C12 C C12 R N N 0 -1.321 -0.884 1.242
9 C13 C C13 N N N 0 -1.732 0.231 2.181
10 N14 N N14 N N N 0 -0.697 -1.186 -6.242
11 O15 O O15 N N N 0 -1.924 -0.826 -1.383
12 C16 C C16 R N N 0 -0.624 -1.51 2.452
13 S17 S S17 N N N 0 1.211 -1.484 2.357
14 O18 O O18 N N N 0 -2.469 1.188 2.08
15 O19 O O19 N N N 0 0.702 1.93 -7.468
16 O20 O O20 N N N 0 1.377 -0.167 -7.63
17 N29 N N29 N N N 0 -0.944 -0.279 3.215
18 C30 C C30 S N N 0 0.205 0.54 3.615
19 C31 C C31 N N N 0 -0.109 1.224 4.92
20 C32 C C32 N N N 0 1.496 -0.312 3.758
21 C33 C C33 N N N 0 1.542 -1.041 5.102
22 C37 C C37 N N N 0 2.754 0.531 3.538
23 O42 O O42 N N N 0 0.458 2.404 5.214
24 O43 O O43 N N N 0 -0.873 0.709 5.703
25 H2 H H2 N N N 0 -1.169 0.848 -6.012
26 H32 H 2H3 N N N 0 0.712 1.341 -4.474
27 H31 H 1H3 N N N 0 1.289 -0.333 -4.644
28 H42A H 2H4 N N N 0 -0.855 -1.166 -3.72
29 H41 H 1H4 N N N 0 -1.433 0.508 -3.551
30 H72 H 2H7 N N N 0 0.448 1.001 -2.013
31 H71 H 1H7 N N N 0 1.026 -0.673 -2.183
32 H11 H H11 N N N 0 0.498 -0.172 0.411
33 H12 H H12 N N N 0 -2.158 -1.471 0.866
34 H142 H 2H14 N N N 0 0.145 -1.741 -6.229
35 H141 H 1H14 N N N 0 -1.243 -1.467 -5.442
36 H16 H H16 N N N 0 -1.054 -2.44 2.822
37 H19 H H19 N N N 0 1.31 2.21 -8.165
38 H30 H H30 N N N 0 0.384 1.297 2.852
39 H333 H 3H33 N N N 0 2.417 -1.691 5.133
40 H332 H 2H33 N N N 0 1.603 -0.311 5.91
41 H331 H 1H33 N N N 0 0.64 -1.641 5.221
42 H373 H 3H37 N N N 0 3.632 -0.113 3.564
43 H372 H 2H37 N N N 0 2.694 1.026 2.569
44 H371 H 1H37 N N N 0 2.83 1.281 4.325
45 H42 H H42 N N N 0 0.255 2.843 6.052



IP1 : Chemical Bonds

Total Number of Bonds: 46
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.51 N N
2 C1 O19 C O sing 1.34 N N
3 C1 O20 C O doub 1.21 N N
4 C2 C3 C C sing 1.53 N N
5 C2 N14 C N sing 1.47 N N
6 C2 H2 C H sing 1.09 N N
7 C3 C4 C C sing 1.53 N N
8 C3 H32 C H sing 1.09 N N
9 C3 H31 C H sing 1.09 N N
10 C4 C7 C C sing 1.53 N N
11 C4 H42A C H sing 1.09 N N
12 C4 H41 C H sing 1.09 N N
13 C7 C10 C C sing 1.51 N N
14 C7 H72 C H sing 1.09 N N
15 C7 H71 C H sing 1.09 N N
16 C10 N11 C N sing 1.35 N N
17 C10 O15 C O doub 1.21 N N
18 N11 C12 N C sing 1.46 N N
19 N11 H11 N H sing 0.97 N N
20 C12 C13 C C sing 1.51 N N
21 C12 C16 C C sing 1.53 N N
22 C12 H12 C H sing 1.09 N N
23 C13 O18 C O doub 1.21 N N
24 C13 N29 C N sing 1.4 N N
25 N14 H142 N H sing 1.01 N N
26 N14 H141 N H sing 1.01 N N
27 C16 S17 C S sing 1.84 N N
28 C16 N29 C N sing 1.48 N N
29 C16 H16 C H sing 1.09 N N
30 S17 C32 S C sing 1.85 N N
31 O19 H19 O H sing 0.97 N N
32 N29 C30 N C sing 1.47 N N
33 C30 C31 C C sing 1.51 N N
34 C30 C32 C C sing 1.55 N N
35 C30 H30 C H sing 1.09 N N
36 C31 O42 C O sing 1.34 N N
37 C31 O43 C O doub 1.21 N N
38 C32 C33 C C sing 1.53 N N
39 C32 C37 C C sing 1.53 N N
40 C33 H333 C H sing 1.09 N N
41 C33 H332 C H sing 1.09 N N
42 C33 H331 C H sing 1.09 N N
43 C37 H373 C H sing 1.09 N N
44 C37 H372 C H sing 1.09 N N
45 C37 H371 C H sing 1.09 N N
46 O42 H42 O H sing 0.97 N N



IP1 : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
IP1 1qje Open in New Window Bound ligand 1 1
IP1 6y0p Open in New Window Bound ligand 1 1
IP1 6zao Open in New Window Bound ligand 1 1
IP1 6zaq Open in New Window Bound ligand 1 1