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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "ligase/ligase inhibitor"

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Search Summary

This query matches 246 Structures.

Refinements

Structure Determination Methodology

experimental (246)

Scientific Name of Source Organism

	Homo sapiens (91)
	Mycobacterium tuberculosis (30)
	Trypanosoma brucei brucei TREU927 (19)
	Trypanosoma cruzi strain CL Brener (18)
	Trypanosoma brucei (15)
	Toxoplasma gondii (10)
	Escherichia coli K-12 (7)
	Tequatrovirus T4 (6)
	Staphylococcus aureus A9781 (5)
	Xenopus laevis (5)

More...

Taxonomy

	Eukaryota (171)
	Bacteria (72)
	Duplodnaviria (6)
	Eukaryota (eukaryotes) (4)
	other sequences (4)

Experimental Method

	X-RAY DIFFRACTION (245)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (246)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (12)
	1.5 - 2.0 (75)
	2.0 - 2.5 (94)
	2.5 - 3.0 (53)
	3.0 - 3.5 (11)
	3.5 - 4.0 (1)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (118)
	2015 - 2019 (83)
	2020 - 2024 (43)

Enzyme Classification Name

	Ligases (224)
	Transferases (76)
	Hydrolases (6)

Symmetry Type

	Asymmetric (152)
	Cyclic (102)
	Dihedral (4)

SCOP Classification

	All alpha proteins (76)
	Alpha and beta proteins (a/b) (75)
	Alpha and beta proteins (a+b) (35)
	Artifacts (52)
	All beta proteins (9)
	Small proteins (7)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 25 of 246 Structures

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2AST \| pdb_00002ast	Download File View File

Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide

Hao, B., Zhang, N., Schulman, B.A., Wu, G., Pagano, M., Pavletich, N.P.

(2005) Mol Cell 20: 9-19

Released	2005-10-18
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-dependent kinase inhibitor 1B (protein) Cyclin-dependent kinases regulatory subunit 1 (protein) S-phase kinase-associated protein 1A (protein) S-phase kinase-associated protein 2 (protein)
Unique Ligands	BEN

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2AXI \| pdb_00002axi	Download File View File

HDM2 in complex with a beta-hairpin

Mittl, P.R.E., Fasan, R., Robinson, J., Gruetter, M.G.

(2006) Chembiochem 7: 515-526

Released	2006-03-21
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-protein ligase E3 Mdm2 (protein) cyclic 8-mer peptide (protein)
Unique Ligands	MPO, SO4

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3IWY \| pdb_00003iwy	Download File View File

Crystal structure of human MDM2 complexed with D-peptide (12 residues)

Pazgier, M., Lu, W.

(2010) Proc Natl Acad Sci U S A 398: 200-213

Released	2010-04-21
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Homo sapiens
Macromolecule	D-peptide inhibitor (protein) E3 ubiquitin-protein ligase Mdm2 (protein)

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3LNJ \| pdb_00003lnj	Download File View File

Crystal structure of human MDM2 in complex with D-peptide inhibitor (DPMI-alpha)

Pazgier, M., Lu, W.

(2010) Angew Chem Int Ed Engl 49: 3649-3652

Released	2010-03-09
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	D-peptide inhibitor (protein) E3 ubiquitin-protein ligase Mdm2 (protein)
Unique Ligands	CL, GOL, SO4

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3LNZ \| pdb_00003lnz	Download File View File

Crystal structure of human MDM2 with a 12-mer peptide inhibitor PMI (N8A mutant)

Pazgier, M., Lu, W.

(2010) J Mol Biology 398: 200-213

Released	2010-03-09
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	12-mer peptide inhibitor (protein) E3 ubiquitin-protein ligase Mdm2 (protein)
Unique Ligands	CL

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3PN1 \| pdb_00003pn1	Download File View File

Novel Bacterial NAD+-dependent DNA Ligase Inhibitors with Broad Spectrum Potency and Antibacterial Efficacy In Vivo

Mills, S., Eakin, A., Buurman, E., Newman, J., Gao, N., Huynh, H., Johnson, K., Lahiri, S., Shapiro, A., Walkup, G., Wei, Y., Stokes, S.

(2011) Antimicrob Agents Chemother 55: 1088-1096

Released	2011-01-12
Method	X-RAY DIFFRACTION 2 Å
Organisms	Haemophilus influenzae
Macromolecule	DNA ligase (protein)
Unique Ligands	IVH, IWH

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3RUX \| pdb_00003rux	Download File View File

Crystal structure of biotin-protein ligase BirA from Mycobacterium tuberculosis in complex with an acylsulfamide bisubstrate inhibitor

Geders, T.W., Finzel, B.C.

(2011) Chem Biol 18: 1432-1441

Released	2011-12-14
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	BirA bifunctional protein (protein)
Unique Ligands	BS5

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3RZ3 \| pdb_00003rz3	Download File View File

Human Cdc34 E2 in complex with CC0651 inhibitor

Ceccarelli, D.F., Webb, D.R., Sicheri, F.

(2011) Cell 145: 1075-1087

Released	2011-07-06
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 R1 (protein)
Unique Ligands	U94

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3TDC \| pdb_00003tdc	Download File View File

Crystal Structure of Human Acetyl-CoA carboxylase 2

Dougan, D.R., Mol, C.D.

(2011) Bioorg Med Chem Lett 21: 6314-6318

Released	2011-10-12
Method	X-RAY DIFFRACTION 2.41 Å
Organisms	Homo sapiens
Macromolecule	Acetyl-CoA carboxylase 2 variant (protein)
Unique Ligands	0EU

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3TPX \| pdb_00003tpx	Download File View File

Crystal structure of human MDM2 in complex with a trifluoromethylated D-peptide inhibitor

Wu, X., Pazgier, M.

(2012) J Med Chem 55: 6237-6241

Released	2012-06-20
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	D-peptide inhibitor DPMI-delta (protein) E3 ubiquitin-protein ligase Mdm2 (protein)
Unique Ligands	ACT, CL, SO4

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3V3B \| pdb_00003v3b	Download File View File

Structure of the Stapled p53 Peptide Bound to Mdm2

Baek, S., Kutchukian, P.S., Verdine, G.L., Huber, R., Holak, T.A., Ki Won, L., Popowicz, G.M.

(2012) J Am Chem Soc 134: 103-106

Released	2012-01-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase Mdm2 (protein) SAH-p53-8 stapled-peptide (protein)
Unique Ligands	CL

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3V7C \| pdb_00003v7c	Download File View File

Cystal structure of SaBPL in complex with inhibitor

Yap, M.Y., Pendini, N.R.

(2012) J Biological Chem 287: 17823-17832

Released	2012-04-18
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Staphylococcus aureus A9781
Macromolecule	Biotin ligase (protein)
Unique Ligands	C77

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3V7R \| pdb_00003v7r	Download File View File

Crystal structure of Staphylococcus aureus biotin protein ligase in complex with inhibitor

Yap, M.Y., Pendini, N.R.

(2012) J Biological Chem 287: 17823-17832

Released	2012-12-26
Method	X-RAY DIFFRACTION 2.61 Å
Organisms	Staphylococcus aureus A9781
Macromolecule	Biotin ligase (protein)
Unique Ligands	32G

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3V7S \| pdb_00003v7s	Download File View File

Crystal structure of Staphylococcus aureus biotin protein ligase in complex with inhibitor 0364

Yap, M.Y., Pendini, N.R.

(2012) J Biological Chem 287: 17823-17832

Released	2012-04-25
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Staphylococcus aureus A9781
Macromolecule	Biotin ligase (protein)
Unique Ligands	36F

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3V8K \| pdb_00003v8k	Download File View File

Crystal structure of Staphylococcus aureus biotin protein ligase in complex with biotin

Yap, M.Y., Pendini, N.R.

(2012) J Biological Chem 287: 17823-17832

Released	2012-12-26
Method	X-RAY DIFFRACTION 3.23 Å
Organisms	Staphylococcus aureus A9781
Macromolecule	Biotin ligase (protein)
Unique Ligands	BTN

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3V8L \| pdb_00003v8l	Download File View File

Crystal structure of Staphylococcus aureus biotin protein ligase in complex with biotinyl-5'-AMP

Yap, M.Y.

(2012) J Biological Chem 287: 17823-17832

Released	2012-12-26
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Staphylococcus aureus A9781
Macromolecule	Biotin ligase (protein)
Unique Ligands	BT5

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3VZV \| pdb_00003vzv	Download File View File

Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor

Shimizu, H., Katakura, S., Miyazaki, M., Naito, H., Sugimoto, Y., Kawato, H., Okayama, T., Soga, T.

(2013) Bioorg Med Chem Lett 23: 728-732

Released	2013-02-06
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase Mdm2 (protein)
Unique Ligands	VZV

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3W69 \| pdb_00003w69	Download File View File

Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor

Shimizu, H., Katakura, S., Miyazaki, M., Naito, H., Sugimoto, Y., Kawato, H., Okayama, T., Soga, T.

(2013) Bioorg Med Chem 21: 4319-4331

Released	2013-06-05
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase Mdm2 (protein)
Unique Ligands	LTZ, SO4

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4DDH \| pdb_00004ddh	Download File View File

Pantothenate synthetase in complex with 6-methoxy-1-benzofuran-3-yl acetic acid

Silvestre, H.L.

(2013) Proc Natl Acad Sci U S A 110: 12984-12989

Released	2013-02-13
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Pantothenate synthetase (protein)
Unique Ligands	EDO, EOH, GOL, MS0

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4DDK \| pdb_00004ddk	Download File View File

Pantothenate synthetase in complex with 1,3-benzodioxole-5-carboxylic acid

Silvestre, H.L.

(2013) Proc Natl Acad Sci U S A 110: 12984-12989

Released	2013-02-13
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Pantothenate synthetase (protein)
Unique Ligands	0HN, EDO, EOH, GOL

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4DDM \| pdb_00004ddm	Download File View File

Pantothenate synthetase in complex with 2,1,3-benzothiadiazole-5-carboxylic acid

Silvestre, H.L.

(2013) Proc Natl Acad Sci U S A 110: 12984-12989

Released	2013-02-13
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Pantothenate synthetase (protein)
Unique Ligands	0HO, EDO, EOH, GOL

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4DE5 \| pdb_00004de5	Download File View File

Pantothenate synthetase in complex with fragment 6

Silvestre, H.L.

(2013) Proc Natl Acad Sci U S A 110: 12984-12989

Released	2013-03-06
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Pantothenate synthetase (protein)
Unique Ligands	0JD, EDO, EOH, GOL

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4DIJ \| pdb_00004dij	Download File View File

The Central Valine Concept Provides an Entry in a New Class of Non Peptide Inhibitors of the P53-MDM2 Interaction

Kallen, J.

(2012) Bioorg Med Chem Lett 22: 3498-3502

Released	2012-05-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase Mdm2 (protein)
Unique Ligands	BLF

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4EEQ \| pdb_00004eeq	Download File View File

Crystal structure of E. faecalis DNA ligase with inhibitor

Wang, T., Charifson, P., Wei, Y.

To be published

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Enterococcus faecalis
Macromolecule	DNA ligase (protein)
Unique Ligands	0OX, NMN, SO4

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4EF6 \| pdb_00004ef6	Download File View File

Crystal Structure of Mycobacterium tuberculosis Pantothenate synthetase in complex with fragment 1

Silvestre, H.L., Ciulli, A., Abell, C., Blundell, T.

(2013) Proc Natl Acad Sci U S A 110: 12984-12989

Released	2013-03-13
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Pantothenate synthetase (protein)
Unique Ligands	EDO, EOH, GOL, I2E

1 to 25 of 246 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

2AST | pdb_00002ast

2AXI | pdb_00002axi

3IWY | pdb_00003iwy

3LNJ | pdb_00003lnj

3LNZ | pdb_00003lnz

3PN1 | pdb_00003pn1

3RUX | pdb_00003rux

3RZ3 | pdb_00003rz3

3TDC | pdb_00003tdc

3TPX | pdb_00003tpx

3V3B | pdb_00003v3b

3V7C | pdb_00003v7c

3V7R | pdb_00003v7r

3V7S | pdb_00003v7s

3V8K | pdb_00003v8k

3V8L | pdb_00003v8l

3VZV | pdb_00003vzv

3W69 | pdb_00003w69

4DDH | pdb_00004ddh

4DDK | pdb_00004ddk

4DDM | pdb_00004ddm

4DE5 | pdb_00004de5

4DIJ | pdb_00004dij

4EEQ | pdb_00004eeq

4EF6 | pdb_00004ef6