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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Mandal, M."

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Search Summary

This query matches 25 Structures.

Refinements

Structure Determination Methodology

experimental (25)

Scientific Name of Source Organism

	Homo sapiens (14)
	Pseudomonas aeruginosa (5)
	Klebsiella pneumoniae (4)
	Escherichia coli K-12 (2)
	Staphylococcus phage GRCS (2)

Taxonomy

	Eukaryota (14)
	Bacteria (11)
	Duplodnaviria (2)

Experimental Method

X-RAY DIFFRACTION (25)

Polymer Entity Type

Protein (25)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (9)
	1.5 - 2.0 (14)
	2.0 - 2.5 (1)

Release Date

	2010 - 2014 (6)
	2015 - 2019 (8)
	2020 - 2024 (10)
	2025 - 2029 (1)

Enzyme Classification Name

Hydrolases (19)

Symmetry Type

Asymmetric (25)

SCOP Classification

All beta proteins (6)

AllSelected

1 to 25 of 25 Structures

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4H1E \| pdb_00004h1e	Download File View File

Structure of BACE-1 Bound to (7aR)-6-benzoyl-7a-(4-(3-cyanophenyl)thiophen-2-yl)-3-methyl-4-oxohexahydro-1H-pyrrolo[3,4-d]pyrimidin-2(3H)-iminium

Orth, P.

(2012) J Med Chem 55: 9331-9345

Released	2012-10-17
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	10J

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4H3F \| pdb_00004h3f	Download File View File

Structure of BACE Bound to 3-(5-((7aR)-2-imino-6-(6-methoxypyridin-2-yl)-3-methyl-4-oxooctahydro-1H-pyrrolo[3,4-d]pyrimidin-7a-yl)thiophen-3-yl)benzonitrile

Strickland, C., Mandal, M.

(2012) J Med Chem 55: 9331-9345

Released	2012-11-07
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	10O, TLA

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4H3G \| pdb_00004h3g	Download File View File

Structure of BACE Bound to 2-((7aR)-7a-(4-(3-cyanophenyl)thiophen-2-yl)-2-imino-3-methyl-4-oxohexahydro-1H-pyrrolo[3,4-d]pyrimidin-6(2H)-yl)nicotinonitrile

Strickland, C., Mandal, M.

(2012) J Med Chem 55: 9331-9345

Released	2012-11-07
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	10Q, TLA

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4H3I \| pdb_00004h3i	Download File View File

Structure of BACE Bound to 3-(5-((7aR)-2-imino-6-(3-methoxypyridin-2-yl)-3-methyl-4-oxooctahydro-1H-pyrrolo[3,4-d]pyrimidin-7a-yl)thiophen-3-yl)benzonitrile

Strickland, C., Mandal, M.

(2012) J Med Chem 55: 9331-9345

Released	2012-11-07
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	10V, TLA

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4H3J \| pdb_00004h3j	Download File View File

Structure of BACE Bound to 2-fluoro-5-(5-(2-imino-3-methyl-4-oxo-6-phenyloctahydro-1H-pyrrolo[3,4-d]pyrimidin-7a-yl)thiophen-2-yl)benzonitrile

Strickland, C., Mandal, M.

(2012) J Med Chem 55: 9331-9345

Released	2012-10-17
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	10W, TLA

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4HA5 \| pdb_00004ha5	Download File View File

Structure of BACE Bound to (S)-3-(5-(2-imino-1,4-dimethyl-6-oxohexahydropyrimidin-4-yl)thiophen-3-yl)benzonitrile

Strickland, C., Mandal, M.

(2012) J Med Chem 55: 9331-9345

Released	2012-10-17
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	13W, TLA

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5HD0 \| pdb_00005hd0	Download File View File

BACE-1 in complex with (7aR)-7a-(4-(3-cyanophenyl)thiophen-2-yl)-6-(5-fluoropyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-pyrrolo[3,4-d]pyrimidin-2-iminium

Orth, P.

(2016) J Med Chem 59: 3231-3248

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	60Y, TLA

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5HDU \| pdb_00005hdu	Download File View File

BACE-1 incomplex with (7aR)-7a-(4-(3-cyanophenyl)thiophen-2-yl)-6-(5-fluoro-4-methoxypyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-pyrrolo[3,4-d]pyrimidin-2-iminium

Orth, P.

(2016) J Med Chem 59: 3231-3248

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	60W, TLA

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5HDV \| pdb_00005hdv	Download File View File

BACE-1 incomplex with (7aR)-7a-(5-cyanothiophen-2-yl)-6-(5-fluoro-4-methoxy-6-methylpyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-pyrrolo[3,4-d]pyrimidin-2-iminium

Orth, P.

(2016) J Med Chem 59: 3231-3248

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.71 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	60V, TLA

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5HDX \| pdb_00005hdx	Download File View File

BACE-1 in complex with (7aR)-7a-(5-cyanothiophen-2-yl)-6-(4-ethoxy-5-fluoro-6-methylpyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-pyrrolo[3,4-d]pyrimidin-2-iminium

Orth, P.

(2016) J Med Chem 59: 3231-3248

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.602 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	60U

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5HDZ \| pdb_00005hdz	Download File View File

BACE-1 in complex with (7aR)-7a-(5-cyanothiophen-2-yl)-6-(5-fluoro-4-methyl-6-(methylthio)pyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-pyrrolo[3,4-d]pyrimidin-2-iminium

Orth, P.

(2016) J Med Chem 59: 3231-3248

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.49 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	954

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5HE4 \| pdb_00005he4	Download File View File

BACE-1 in complex with (4aR,7aS)-7a-(2,6-difluorophenyl)-6-(5-fluoro-4-methoxy-6-methylpyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-pyrrolo[3,4-d]pyrimidin-2-iminium

Orth, P.

(2016) J Med Chem 59: 3231-3248

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.53 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	60T, TLA

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5HE5 \| pdb_00005he5	Download File View File

BACE-1 in complex with (7aR)-7a-(5-cyanothiophen-2-yl)-6-(5-fluoro-4-methyl-6-(methylamino)pyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-pyrrolo[3,4-d]pyrimidin-2-iminium

Orth, P.

(2016) J Med Chem 59: 3231-3248

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	60S, TLA

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5HE7 \| pdb_00005he7	Download File View File

BACE-1 in complex with (4aR,7aS)-7a-(2,4-difluorophenyl)-6-(5-fluoro-4-methoxy-6-methylpyrimidin-2-yl)-2-imino-3-methyloctahydro-4H-pyrrolo[3,4-d]pyrimidin-4-one

Orth, P.

(2016) J Med Chem 59: 3231-3248

Released	2016-03-16
Method	X-RAY DIFFRACTION 1.71 Å
Organisms	Homo sapiens
Macromolecule	Beta-secretase 1 (protein)
Unique Ligands	60X

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7UOX \| pdb_00007uox	Download File View File

NDM1-inhibitor co-structure

Scapin, G., Fischmann, T.O.

(2022) J Med Chem 65: 16234-16251

Released	2023-03-08
Method	X-RAY DIFFRACTION 0.99 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Metallo beta-lactamase (protein)
Unique Ligands	ACT, CA, CD, O0L, ZN

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7UOY \| pdb_00007uoy	Download File View File

NDM1-inhibitor co-structure

Scapin, G., Fischmann, T.O.

(2022) J Med Chem 65: 16234-16251

Released	2023-03-08
Method	X-RAY DIFFRACTION 1.47 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Metallo beta-lactamase (protein)
Unique Ligands	CD, O0F, ZN

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7UP1 \| pdb_00007up1	Download File View File

NDM1-inhibitor co-structure

Scapin, G., Fischmann, T.O.

(2022) J Med Chem 65: 16234-16251

Released	2023-03-08
Method	X-RAY DIFFRACTION 1.11 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Metallo beta-lactamase (protein)
Unique Ligands	CD, NZR, ZN

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7UP2 \| pdb_00007up2	Download File View File

NDM1-inhibitor co-structure

Scapin, G., Fischmann, T.O.

(2022) J Med Chem 65: 16234-16251

Released	2023-03-08
Method	X-RAY DIFFRACTION 1.13 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Beta-lactamase VIM-1 (protein)
Unique Ligands	NZR, ZN

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7UP3 \| pdb_00007up3	Download File View File

NDM1-inhibitor co-structure

Scapin, G., Fischmann, T.O.

(2022) J Med Chem 65: 16234-16251

Released	2023-03-08
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Klebsiella pneumoniae
Macromolecule	Metallo beta-lactamase (protein)
Unique Ligands	CD, EPE, NZ0, ZN

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7UYA \| pdb_00007uya	Download File View File

Inhibitor bound VIM1

Fischmann, T.O., Scapin, G.

(2024) J Med Chem 67: 3400-3418

Released	2023-05-24
Method	X-RAY DIFFRACTION 1.01 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Beta-lactamase VIM-1 (protein)
Unique Ligands	OKC, ZN

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7UYB \| pdb_00007uyb	Download File View File

Inhibitor bound VIM1

Fischmann, T.O., Scapin, G.

(2024) J Med Chem 67: 3400-3418

Released	2023-05-24
Method	X-RAY DIFFRACTION 1.11 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Beta-lactamase VIM-1 (protein)
Unique Ligands	OK0, ZN

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7UYC \| pdb_00007uyc	Download File View File

Inhibitor bound VIM1

Fischmann, T.O., Scapin, G.

(2024) J Med Chem 67: 3400-3418

Released	2023-05-24
Method	X-RAY DIFFRACTION 1.02 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Beta-lactamase VIM-1 (protein)
Unique Ligands	MG, OJR, ZN

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7UYD \| pdb_00007uyd	Download File View File

Inhibitor bound VIM1

Fischmann, T.O., Scapin, G.

(2024) J Med Chem 67: 3400-3418

Released	2023-05-24
Method	X-RAY DIFFRACTION 1 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Metallo-beta-lactamase VIM-2-like protein (protein)
Unique Ligands	ACT, EDO, ZN

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8H1I \| pdb_00008h1i	Download File View File

Crystal structure of PlyGRCS, a bacteriophage Endolysin in complex with Cold shock protein C

Padmanabhan, B., Gopinatha, K., Mandal, M., Saranya, G., Sudhagar, B.

To be published

Released	2023-10-18
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli K-12 Staphylococcus phage GRCS
Macromolecule	Cold shock-like protein CspC (protein) Endolysin (protein)
Unique Ligands	CA, MES

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8XYF \| pdb_00008xyf	Download File View File

Crystal structure of Holo-PlyGRCS, a bacteriophage Endolysin in complex with Cold shock protein C

Padmanabhan, B., Gopinath, K., Harshitha, H.N.

(2025) Proteins 93: 920-933

Released	2025-01-01
Method	X-RAY DIFFRACTION 1.67 Å
Organisms	Escherichia coli K-12 Staphylococcus phage GRCS
Macromolecule	Cold shock-like protein CspC (protein) Endolysin (protein)
Unique Ligands	MES

1 to 25 of 25 Structures

Page 1 of 1

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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

4H1E | pdb_00004h1e

4H3F | pdb_00004h3f

4H3G | pdb_00004h3g

4H3I | pdb_00004h3i

4H3J | pdb_00004h3j

4HA5 | pdb_00004ha5

5HD0 | pdb_00005hd0

5HDU | pdb_00005hdu

5HDV | pdb_00005hdv

5HDX | pdb_00005hdx

5HDZ | pdb_00005hdz

5HE4 | pdb_00005he4

5HE5 | pdb_00005he5

5HE7 | pdb_00005he7

7UOX | pdb_00007uox

7UOY | pdb_00007uoy

7UP1 | pdb_00007up1

7UP2 | pdb_00007up2

7UP3 | pdb_00007up3

7UYA | pdb_00007uya

7UYB | pdb_00007uyb

7UYC | pdb_00007uyc

7UYD | pdb_00007uyd

8H1I | pdb_00008h1i

8XYF | pdb_00008xyf