Binding Site Information of Target

Target General Information

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Target ID

T89034

Target Info

Target Name

Plasminogen (PLG)

Synonyms

Plasmin

Target Type

Successful Target

Gene Name

PLG

Biochemical Class

Peptidase

UniProt ID

PLMN_HUMAN

Drug Binding Sites of Target

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Ligand Name: Aminocaproic acid

Ligand Info

Structure Description

THE STRUCTURE OF THE NON-COVALENT COMPLEX OF RECOMBINANT KRINGLE 1 DOMAIN OF HUMAN PLASMINOGEN WITH EACA (EPSILON-AMINOCAPROIC ACID)

PDB:1CEA

Method

X-ray diffraction

Resolution

2.06 Å

Mutation

[1]

PDB Sequence

ECKTGNGKNY

⁹

RGTMSKTKNG

¹⁹

ITCQKWSSTS

²⁹

PHRPRFSPAT

³⁹

HPSEGLEENY

⁴⁹

CRNPDNDPQG

⁵⁹

PWCYTTDPEK

⁶⁹

RYDYCDILEC

⁷⁹

Residue

Distance (Å)

ARG34

2.697

PHE35

3.729

ASP54

3.007

ASP56

2.986

TRP61

3.453

Residue

Distance (Å)

TYR63

2.603

ARG70

3.049

TYR71

3.723

TYR73

4.172

Click to View More Binding Site Information of This Target and Ligand Pair

Ligand Name: Tranexamic acid

Ligand Info

Structure Description

THE STRUCTURE OF THE NON-COVALENT COMPLEX OF RECOMBINANT KRINGLE 1 DOMAIN OF HUMAN PLASMINOGEN WITH AMCHA (TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID)

PDB:1CEB

Method

X-ray diffraction

Resolution

2.07 Å

Mutation

[1]

PDB Sequence

ECKTGNGKNY

⁹

RGTMSKTKNG

¹⁹

ITCQKWSSTS

²⁹

PHRPRFSPAT

³⁹

HPSEGLEENY

⁴⁹

CRNPDNDPQG

⁵⁹

PWCYTTDPEK

⁶⁹

RYDYCDILEC

⁷⁹

Residue

Distance (Å)

ARG34

2.665

PHE35

3.746

ASP54

2.722

ASP56

3.052

TRP61

3.534

Residue

Distance (Å)

TYR63

2.507

ARG70

2.688

TYR71

3.500

TYR73

4.319

Click to View More Binding Site Information of This Target and Ligand Pair

Ligand Name: Nalpha-[trans-4-(Aminomethyl)cyclohexane-1-Carbonyl]-N-Octyl-O-[(Quinolin-2-Yl)methyl]-L-Tyrosinamide

Ligand Info

Structure Description

Protease Inhibitor

PDB:5UGG

Method

X-ray diffraction

Resolution

1.20 Å

Mutation

[2]

PDB Sequence

PSFDCGKPQV

⁵⁵³

EPKKCPVVGG

⁵⁶⁵

CVAHPHSWPW

⁵⁷⁵

QVSLRTRFGM

⁵⁸⁵

HFCGGTLISP

⁵⁹⁵

EWVLTAAHCL

⁶⁰⁵

EKSPRPSSYK

⁶¹⁵

VILGAHQEVN

⁶²⁵

LEPHVQEIEV

⁶³⁵

SRLFLEPTRK

⁶⁴⁵

DIALLKLSSP

⁶⁵⁵

AVITDKVIPA

⁶⁶⁵

CLPSPNYVVA

⁶⁷⁵

DRTECFITGW

⁶⁸⁵

GETQGTFGAG

⁶⁹⁵

LLKEAQLPVI

⁷⁰⁵

ENKVCNRYEF

⁷¹⁵

LNGRVQSTEL

⁷²⁵

CAGHLAGGTD

⁷³⁵

SCQGDSGGPL

⁷⁴⁵

VCFEKDKYIL

⁷⁵⁵

QGVTSWGLGC

⁷⁶⁵

ARPNKPGVYV

⁷⁷⁵

RVSRFVTWIE

⁷⁸⁵

GVMRNN

Click to Show 3D Structure of This Binding Site

set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .89M or .89M2 or .89M3 or :389M;style chemicals stick;color identity;select .A:581 or .A:586 or .A:587 or .A:588 or .A:603 or .A:604 or .A:607 or .A:608 or .A:610 or .A:613 or .A:614 or .A:735 or .A:736 or .A:737 or .A:738 or .A:739 or .A:740 or .A:741 or .A:759 or .A:760 or .A:761 or .A:762 or .A:764 or .A:765 or .A:772 or .A:774; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all

Residue

Distance (Å)

THR581

4.944

HIS586

4.779

PHE587

3.561

CYS588

3.563

HIS603

3.437

CYS604

4.235

LYS607

3.120

SER608

4.240

ARG610

4.760

SER613

4.686

TYR614

4.449

ASP735

3.068

SER736

2.924

Residue

Distance (Å)

CYS737

3.342

GLN738

3.252

GLY739

2.949

ASP740

3.654

SER741

3.263

THR759

3.732

SER760

4.303

TRP761

3.893

GLY762

3.723

GLY764

3.459

CYS765

4.352

GLY772

3.921

TYR774

4.692

Ligand Name: Nalpha-[trans-4-(Aminomethyl)cyclohexane-1-Carbonyl]-N-Octyl-O-[(Pyridin-4-Yl)methyl]-L-Tyrosinamide

Ligand Info

Structure Description

Protease Inhibitor

PDB:5UGD

Method

X-ray diffraction

Resolution

1.38 Å

Mutation

[2]

PDB Sequence

PSFDCGKPQV

⁵⁵³

EPKKCPVVGG

⁵⁶⁵

CVAHPHSWPW

⁵⁷⁵

QVSLRTRFGM

⁵⁸⁵

HFCGGTLISP

⁵⁹⁵

EWVLTAAHCL

⁶⁰⁵

EKSPRPSSYK

⁶¹⁵

VILGAHQEVN

⁶²⁵

LEPHVQEIEV

⁶³⁵

SRLFLEPTRK

⁶⁴⁵

DIALLKLSSP

⁶⁵⁵

AVITDKVIPA

⁶⁶⁵

CLPSPNYVVA

⁶⁷⁵

DRTECFITGW

⁶⁸⁵

GETQGTFGAG

⁶⁹⁵

LLKEAQLPVI

⁷⁰⁵

ENKVCNRYEF

⁷¹⁵

LNGRVQSTEL

⁷²⁵

CAGHLAGGTD

⁷³⁵

SCQGDSGGPL

⁷⁴⁵

VCFEKDKYIL

⁷⁵⁵

QGVTSWGLGC

⁷⁶⁵

ARPNKPGVYV

⁷⁷⁵

RVSRFVTWIE

⁷⁸⁵

GVMRNN

Click to Show 3D Structure of This Binding Site

set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .89S or .89S2 or .89S3 or :389S;style chemicals stick;color identity;select .A:581 or .A:586 or .A:587 or .A:588 or .A:603 or .A:604 or .A:607 or .A:735 or .A:736 or .A:737 or .A:738 or .A:739 or .A:740 or .A:741 or .A:759 or .A:760 or .A:761 or .A:762 or .A:764 or .A:765 or .A:772 or .A:774; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all

Residue

Distance (Å)

THR581

3.876

HIS586

4.717

PHE587

3.458

CYS588

3.825

HIS603

3.422

CYS604

4.458

LYS607

3.356

ASP735

3.085

SER736

2.918

CYS737

3.323

GLN738

3.308

Residue

Distance (Å)

GLY739

2.941

ASP740

3.610

SER741

3.209

THR759

3.668

SER760

4.211

TRP761

3.829

GLY762

3.687

GLY764

3.589

CYS765

4.370

GLY772

3.854

TYR774

4.713

Ligand Name: L-Alpha-Glutamyl-N-{(1s)-4-{[amino(Iminio)methyl]amino}-1-[(1s)-2-Chloro-1-Hydroxyethyl]butyl}glycinamide

Ligand Info

Structure Description

Structure of the ternary microplasmin-staphylokinase-microplasmin complex: a proteinase-cofactor-substrate complex in action

PDB:1BUI

Method

X-ray diffraction

Resolution

2.65 Å

Mutation

[3]

PDB Sequence

PSFDCGKPQV

⁶

EPKKCPGVVG

¹⁸

GCVAHPHSWP

²⁸

WQVSLRTRFG

³⁸

MHFCGGTLIS

⁴⁸

PEWVLTAAHC

⁵⁸

LEKSPRPSSY

⁶⁴

KVILGAHQEV

⁷⁴

NLEPHVQEIE

⁸⁴

VSRLFLEPTR

⁹⁴

KDIALLKLSS

¹¹⁰

PAVITDKVIP

¹²⁰

ACLPSPNYVV

¹³⁰

ADRTECFITG

¹⁴⁰

WGETQGTFGA

¹⁵²

GLLKEAQLPV

¹⁶²

IENKVCNRYE

^170B

FLNGRVQSTE

¹⁸⁰

LCAGHLAGGT

^188A

DSCQGDSGGP

¹⁹⁸

LVCFEKDKYI

²⁰⁸

LQGVTSWGLG

²¹⁹

CARPNKPGVY

²²⁸

VRVSRFVTWI

²³⁸

EGVMRNN

Click to Show 3D Structure of This Binding Site

set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0GJ or .0GJ2 or .0GJ3 or :30GJ;style chemicals stick;color identity;select .A:41 or .A:42 or .A:57 or .A:58 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:194 or .A:195 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:219 or .A:220 or .A:225 or .A:226 or .A:228; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all

Residue

Distance (Å)

PHE41

4.701

CYS42

4.209

HIS57

1.497

CYS58

4.575

ASP189

3.159

SER190

2.573

CYS191

3.491

GLN192

2.639

GLY193

3.266

ASP194

4.252

SER195

1.381

Residue

Distance (Å)

THR213

4.231

SER214

2.900

TRP215

3.061

GLY216

2.745

LEU217

4.308

GLY219

2.589

CYS220

4.177

PRO225

4.486

GLY226

4.000

TYR228

4.457

Ligand Name: 1-methyl-1H-1,2,3-triazole

Ligand Info

Structure Description

Structure of plasmin and peptide complex

PDB:6Q1U

Method

X-ray diffraction

Resolution

2.35 Å

Mutation

[4]

PDB Sequence

FDCGKPQVEP

⁵⁵⁵

KKCPVVGGCV

⁵⁶⁷

AHPHSWPWQV

⁵⁷⁷

SLRTRFGMHF

⁵⁸⁷

CGGTLISPEW

⁵⁹⁷

VLTAAHCLEK

⁶⁰⁷

SPRPSSYKVI

⁶¹⁷

LGAHQEVNLE

⁶²⁷

PHVQEIEVSR

⁶³⁷

LFLEPTRKDI

⁶⁴⁷

ALLKLSSPAV

⁶⁵⁷

ITDKVIPACL

⁶⁶⁷

PSPNYVVADR

⁶⁷⁷

TECFITGWGE

⁶⁸⁷

TQGTFGAGLL

⁶⁹⁷

KEAQLPVIEN

⁷⁰⁷

KVCNRYEFLN

⁷¹⁷

GRVQSTELCA

⁷²⁷

GHLAGGTDSC

⁷³⁷

QGDSGGPLVC

⁷⁴⁷

FEKDKYILQG

⁷⁵⁷

VTSWGLGCAR

⁷⁶⁷

PNKPGVYVRV

⁷⁷⁷

SRFVTWIEGV

⁷⁸⁷

MRNN

Click to Show 3D Structure of This Binding Site

set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WMH or .WMH2 or .WMH3 or :3WMH;style chemicals stick;color identity;select .A:762; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all

Residue

Distance (Å)

GLY762

4.561

Residue

Distance (Å)

Ligand Name: 5-[(2r,4s)-2-(Phenylmethyl)piperidin-4-Yl]-1,2-Oxazol-3-One

Ligand Info

Structure Description

plasminogen kringle 1 in complex with inhibitor

PDB:4CIK

Method

X-ray diffraction

Resolution

1.78 Å

Mutation

[5]

PDB Sequence

SECKTGNGKN

⁹

YRGTMSKTKN

¹⁹

GITCQKWSST

²⁹

SPHRPRFSPA

³⁹

THPSEGLEEN

⁴⁹

YCRNPDNDPQ

⁵⁹

GPWCYTTDPE

⁶⁹

KRYDYCDILE

⁷⁹

Click to Show 3D Structure of This Binding Site

set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .XO3 or .XO32 or .XO33 or :3XO3;style chemicals stick;color identity;select .A:35 or .A:55 or .A:57 or .A:62 or .A:64 or .A:71 or .A:72 or .A:74; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all

Residue

Distance (Å)

ARG35

2.933

ASP55

2.864

ASP57

2.685

TRP62

3.447

Residue

Distance (Å)

TYR64

2.589

ARG71

2.845

TYR72

3.554

TYR74

4.097

References

Top

REF 1

Crystal structures of the recombinant kringle 1 domain of human plasminogen in complexes with the ligands epsilon-aminocaproic acid and trans-4-(aminomethyl)cyclohexane-1-carboxylic Acid. Biochemistry. 1996 Feb 27;35(8):2567-76.

REF 2

X-ray crystal structure of plasmin with tranexamic acid-derived active site inhibitors. Blood Adv. 2017 May 9;1(12):766-771.

REF 3

The ternary microplasmin-staphylokinase-microplasmin complex is a proteinase-cofactor-substrate complex in action. Nat Struct Biol. 1998 Oct;5(10):917-23.

REF 4

Application and Structural Analysis of Triazole-Bridged Disulfide Mimetics in Cyclic Peptides. Angew Chem Int Ed Engl. 2020 Jul 6;59(28):11273-11277.

REF 5

Discovery of the Fibrinolysis Inhibitor AZD6564, Acting via Interference of a Protein-Protein Interaction. ACS Med Chem Lett. 2014 Feb 18;5(5):538-43.

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