BioLiP

Receptor Information

>5zgr Chain B (length=241) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

EIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLI
VRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGM
DALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGP
LKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHY
AASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR

Ligand ID

ZZ7

InChI

InChI=1S/C16H21N3O5S/c1-16(2)11(15(23)24)19-13(25-16)10(14(21)22)18-12(20)9(17)8-6-4-3-5-7-8/h3-7,9-11,13,19H,17H2,1-2H3,(H,18,20)(H,21,22)(H,23,24)/t9-,10+,11+,13-/m1/s1

InChIKey

KDAWOPKDXRJNHV-MPPDQPJWSA-N

SMILES

Software	SMILES
CACTVS 3.352	CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)[C@H](N)c2ccccc2)C(O)=O
ACDLabs 10.04	O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)N
OpenEye OEToolkits 1.6.1	CC1(C(NC(S1)C(C(=O)O)NC(=O)C(c2ccccc2)N)C(=O)O)C
OpenEye OEToolkits 1.6.1	CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)[C@@H](c2ccccc2)N)C(=O)O)C
CACTVS 3.352	CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)[CH](N)c2ccccc2)C(O)=O

Formula

C16 H21 N3 O5 S

Name

(2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid;
AMPICILLIN (open form)

PDB chain

5zgr Chain B Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	5zgr Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1.
Resolution	1.15 Å
Binding residue (original residue number in PDB)	L65 M67 W93 H122 Q123 D124 H189 C208 K211 N220 H250
Binding residue (residue number reindexed from 1)	L36 M38 W64 H93 Q94 D95 H160 C179 K182 N191 H221
Annotation score	1

Catalytic site (original residue number in PDB)	H120 H122 D124 H189 C208 K211 N220 H250
Catalytic site (residue number reindexed from 1)	H91 H93 D95 H160 C179 K182 N191 H221
Enzyme Commision number	3.5.2.6: beta-lactamase.

	Molecular Function
GO:0008270	zinc ion binding
GO:0008800	beta-lactamase activity
GO:0016787	hydrolase activity
GO:0046872	metal ion binding

	Biological Process
GO:0017001	antibiotic catabolic process
GO:0046677	response to antibiotic

	Cellular Component
GO:0042597	periplasmic space

PDB	RCSB:5zgr, PDBe:5zgr, PDBj:5zgr
PDBsum	5zgr
PubMed	30150473
UniProt	C7C422\|BLAN1_KLEPN Metallo-beta-lactamase type 2 (Gene Name=blaNDM-1)

[Back to BioLiP]

Structure of PDB 5zgr Chain B Binding Site BS03