Target Information

Target General Information

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Target ID

T66686 (Former ID: TTDR00666)

Target Name

Bacterial Penicillin-binding protein 1B (Bact mrcB)

Synonyms

mrcB; PBP1b; PBP-1b; PBP 1b; Murein polymerase

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Gene Name

Bact mrcB

Target Type

Literature-reported target

[1]

Function

Cell wall formation. Synthesis of cross-linked peptidoglycan from the lipid intermediates. The enzyme has a penicillin-insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a penicillin-sensitive transpeptidase C-terminal domain (cross-linking of the peptide subunits).

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BioChemical Class

Acyltransferase

UniProt ID

PBPB_ECOLI

Sequence

MAGNDREPIGRKGKPTRPVKQKVSRRRYEDDDDYDDYDDYEDEEPMPRKGKGKGKGRKPR
GKRGWLWLLLKLAIVFAVLIAIYGVYLDQKIRSRIDGKVWQLPAAVYGRMVNLEPDMTIS
KNEMVKLLEATQYRQVSKMTRPGEFTVQANSIEMIRRPFDFPDSKEGQVRARLTFDGDHL
ATIVNMENNRQFGFFRLDPRLITMISSPNGEQRLFVPRSGFPDLLVDTLLATEDRHFYEH
DGISLYSIGRAVLANLTAGRTVQGASTLTQQLVKNLFLSSERSYWRKANEAYMALIMDAR
YSKDRILELYMNEVYLGQSGDNEIRGFPLASLYYFGRPVEELSLDQQALLVGMVKGASIY
NPWRNPKLALERRNLVLRLLQQQQIIDQELYDMLSARPLGVQPRGGVISPQPAFMQLVRQ
ELQAKLGDKVKDLSGVKIFTTFDSVAQDAAEKAAVEGIPALKKQRKLSDLETAIVVVDRF
SGEVRAMVGGSEPQFAGYNRAMQARRSIGSLAKPATYLTALSQPKIYRLNTWIADAPIAL
RQPNGQVWSPQNDDRRYSESGRVMLVDALTRSMNVPTVNLGMALGLPAVTETWIKLGVPK
DQLHPVPAMLLGALNLTPIEVAQAFQTIASGGNRAPLSALRSVIAEDGKVLYQSFPQAER
AVPAQAAYLTLWTMQQVVQRGTGRQLGAKYPNLHLAGKTGTTNNNVDTWFAGIDGSTVTI
TWVGRDNNQPTKLYGASGAMSIYQRYLANQTPTPLNLVPPEDIADMGVDYDGNFVCSGGM
RILPVWTSDPQSLCQQSEMQQQPSGNPFDQSSQPQQQPQQQPAQQEQKDSDGVAGWIKDM
FGSN

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3D Structure

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PDB

Drug Binding Sites of Target

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Ligand Name: (2R)-3-[[(2R,3R,4R,5S,6S)-3-[(2S,3R,4R,5S,6R)-3-acetamido-5-[(2S,3R,4R,5S,6R)-3-acetamido-4-hydroxy-6-methyl-5-[(2R,3R,4S,5R,6S)-3,4,5-trihydroxy-6-[(2-hydroxy-5-oxocyclopenta-1,3-dien-1-yl)carbamoyl]oxan-2-yl]oxyoxan-2-yl]oxy-4-hydroxy-6-[[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxymethyl]oxan-2-yl]oxy-6-carbamoyl-4-carbamoyloxy-5-hydroxy-5-methyloxan-2-yl]oxy-hydroxyphosphoryl]oxy-2-(3,8,8,14,18-pentamethyl-11-methylidenenonadeca-2,6,13,17-tetraenoxy)propanoic acid

Ligand Info

Structure Description

Crystal Structure of the Full-Length Transglycosylase PBP1b from Escherichia coli

PDB:3VMA

Method

X-ray diffraction

Resolution

2.16 Å

Mutation

[3]

PDB Sequence

LAIVFAVLIA

⁸¹

IYGVYLDQKI

⁹¹

RSRIDGKVWQ

¹⁰¹

LPAAVYGRMV

¹¹¹

NLEPDMTISK

¹²¹

NEMVKLLEAT

¹³¹

QYRQVSKMTR

¹⁴¹

PGEFTVQANS

¹⁵¹

IEMIRRPFDF

¹⁶¹

PDSKEGQVRA

¹⁷¹

RLTFDGDHLA

¹⁸¹

TIVNMENNRQ

¹⁹¹

FGFFRLDPRL

²⁰¹

ITMISSPNGE

²¹¹

QRLFVPRSGF

²²¹

PDLLVDTLLA

²³¹

TEDRHFYEHY

²⁴⁶

SIGRATLTQQ

²⁷¹

LVKNLFLSSE

²⁸¹

RSYWRKANEA

²⁹¹

YMALIMDARY

³⁰¹

SKDRILELYM

³¹¹

NEVYLGQSGD

³²¹

NEIRGFPLAS

³³¹

LYYFGRPVEE

³⁴¹

LSLDQQALLV

³⁵¹

GMVKGASIYN

³⁶¹

PWRNPKLALE

³⁷¹

RRNLVLRLLQ

³⁸¹

QQQIIDQELY

³⁹¹

DMLSARPLVQ

⁴⁰²

PRGGVISPQP

⁴¹²

AFMQLVRQEL

⁴²²

QAKLGDKVKD

⁴³²

LSGVKIFTTF

⁴⁴²

DSVAQDAAEK

⁴⁵²

AAVEGIPALK

⁴⁶²

KQRKLSDLET

⁴⁷²

AIVVVDRFSG

⁴⁸²

EVRAMVGGSE

⁴⁹²

PQFAGYNRAM

⁵⁰²

QARRSIGSLA

⁵¹²

KPATYLTALS

⁵²²

QPKIYRLNTW

⁵³²

IADAPIALRQ

⁵⁴²

PNGQVWSPQN

⁵⁵²

DDRRYSESGR

⁵⁶²

VMLVDALTRS

⁵⁷²

MNVPTVNLGM

⁵⁸²

ALGLPAVTET

⁵⁹²

WIKLGVPKDQ

⁶⁰²

LHPVPAMLLG

⁶¹²

ALNLTPIEVA

⁶²²

QAFQTIASGG

⁶³²

NRAPLSALRS

⁶⁴²

VIAEDGKVLY

⁶⁵²

QSFPQAERAV

⁶⁶²

PAQAAYLTLW

⁶⁷²

TMQQVVQRGT

⁶⁸²

GRQLGAKYPN

⁶⁹²

LHLAGKTGTT

⁷⁰²

NNNVDTWFAG

⁷¹²

IDGSTVTITW

⁷²²

VGRDNNQPTK

⁷³²

LYGASGAMSI

⁷⁴²

YQRYLANQTP

⁷⁵²

TPLNLVPPED

⁷⁶²

IADMGVDYDG

⁷⁷²

NFVCSGGMRI

⁷⁸²

LPVWTSDPQS

⁷⁹²

LCQQSEMQ

Residue

Distance (Å)

GLU233

2.576

GLN271

2.649

LYS274

2.756

ASN275

2.687

SER280

4.383

GLU281

2.591

ARG286

2.747

GLU290

4.541

TYR310

3.975

VAL314

4.129

Residue

Distance (Å)

TYR315

3.371

GLN318

3.669

GLU323

2.676

VAL354

3.011

LYS355

3.057

GLY356

3.792

ALA357

2.919

SER358

2.667

ILE359

3.495

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

Ligand Name: Selenomethionine

Ligand Info

Structure Description

Crystal Structure of the Full-Length Transglycosylase PBP1b from Escherichia coli

PDB:3FWL

Method

X-ray diffraction

Resolution

3.09 Å

Mutation

[3]

PDB Sequence

LWLLLKLAIV

⁷⁵

FAVLIAIYGV

⁸⁵

YLDQKIRSRI

⁹⁵

DGKVWQLPAA

¹⁰⁵

VYGRVNLEPD

¹¹⁶

TISKNEVKLL

¹²⁸

EATQYRQVSK

¹³⁸

TRPGEFTVQA

¹⁴⁹

NSIEIRRPFD

¹⁶⁰

FPDSKEGQVR

¹⁷⁰

ARLTFDGDHL

¹⁸⁰

ATIVNENNRQ

¹⁹¹

FGFFRLDPRL

²⁰¹

ITISSPNGEQ

²¹²

RLFVPRSGFP

²²²

DLLVDTLLAT

²³²

EDRHFYEHDG

²⁴²

ISLYSILTQQ

²⁷¹

LVKNLFLSSE

²⁸¹

RSYWRKANEA

²⁹¹

YALIDARYSK

³⁰³

DRILELYNEV

³¹⁴

YLGQSGDNEI

³²⁴

RGFPLASLYY

³³⁴

FGRPVEELSL

³⁴⁴

DQQALLVGVK

³⁵⁵

GASIYNPWRN

³⁶⁵

PKLALERRNL

³⁷⁵

VLRLLQQQQI

³⁸⁵

IDQELYDLSA

³⁹⁶

RPVISPQPAF

⁴¹⁴

QLVRQELQAK

⁴²⁵

LGDKVKDLSG

⁴³⁵

VKIFTTFDSV

⁴⁴⁵

AQDAAEKAAV

⁴⁵⁵

EGIPALKKQR

⁴⁶⁵

KLSDLETAIV

⁴⁷⁵

VVDRFSGEVR

⁴⁸⁵

AVGGSEPQFA

⁴⁹⁶

GYNRAQARRS

⁵⁰⁷

IGSLAKPATY

⁵¹⁷

LTALSQPKIY

⁵²⁷

RLNTWIADAP

⁵³⁷

IALRQPNGQV

⁵⁴⁷

WSPQNDDRRY

⁵⁵⁷

SESGRVLVDA

⁵⁶⁸

LTRSNVPTVN

⁵⁷⁹

LGALGLPAVT

⁵⁹⁰

ETWIKLGVPK

⁶⁰⁰

DQLHPVPALL

⁶¹¹

GALNLTPIEV

⁶²¹

AQAFQTIASG

⁶³¹

GNRAPLSALR

⁶⁴¹

SVIAEDGKVL

⁶⁵¹

YQSFPQAERA

⁶⁶¹

VPAQAAYLTL

⁶⁷¹

WTQQVVQRGT

⁶⁸²

GRQLGAKYPN

⁶⁹²

LHLAGKTGTT

⁷⁰²

NNNVDTWFAG

⁷¹²

IDGSTVTITW

⁷²²

VGRDNNQPTK

⁷³²

LYGASGASIY

⁷⁴³

QRYLANQTPT

⁷⁵³

PLNLVPPEDI

⁷⁶³

ADGVDYDGNF

⁷⁷⁴

VCSGGRILPV

⁷⁸⁵

WTSDPQSLCQ

⁷⁹⁵

QSE

Residue

Distance (Å)

LEU87

3.556

ILE91

3.494

ILE95

4.634

PRO103

3.414

ALA104

3.314

ALA105

4.256

VAL106

3.806

GLY108

3.774

ARG109

1.325

VAL111

1.328

ASN112

3.565

LEU113

3.835

GLU114

2.988

PRO115

3.087

ASP116

1.328

THR118

1.324

ILE119

3.075

SER120

2.799

LYS121

2.991

ASN122

3.195

GLU123

1.332

VAL125

1.328

LYS126

3.325

LEU127

3.011

LEU128

2.823

TYR133

3.278

VAL136

3.972

SER137

4.495

LYS138

1.332

THR140

1.330

ARG141

4.052

GLU144

3.449

PHE145

3.777

THR146

3.726

ILE152

3.674

GLU153

1.324

ILE155

1.324

ARG156

3.540

PHE159

3.180

ASP160

4.974

PHE161

3.392

PRO162

3.459

VAL169

3.419

ARG170

2.928

ALA171

2.829

ARG172

3.024

LEU173

3.595

PHE175

3.531

ASP178

4.769

HIS179

3.049

LEU180

2.951

VAL184

3.390

ASN185

1.325

GLU187

1.328

ASN188

3.747

ASN189

4.111

PHE195

4.030

ARG196

4.036

LEU197

3.551

ASP198

4.472

PRO199

3.125

LEU201

4.418

ILE202

3.346

THR203

1.329

ILE205

1.335

SER206

3.210

SER207

4.976

GLN212

2.985

ARG213

2.786

LEU214

3.868

PHE221

3.613

LEU225

3.565

VAL226

3.443

LEU229

3.469

GLN270

4.196

LEU272

4.614

VAL273

3.452

LYS274

4.650

PHE277

3.815

LEU278

3.415

ALA288

4.921

ASN289

2.925

GLU290

3.346

ALA291

3.155

TYR292

1.326

ALA294

1.330

LEU295

3.483

ILE296

1.327

ASP298

1.330

ALA299

2.866

ARG300

3.245

TYR301

3.062

ILE306

3.355

LEU307

3.041

GLU308

3.990

LEU309

3.363

TYR310

1.329

ASN312

1.328

GLU313

3.644

VAL314

4.978

TYR315

4.462

LEU316

3.497

GLY326

3.507

PHE327

2.917

PRO328

3.316

LEU329

4.406

TYR334

3.842

PHE335

4.868

ASP345

3.234

GLN346

3.364

LEU349

2.989

LEU350

3.457

VAL351

3.468

GLY352

1.331

VAL354

1.326

LYS355

2.817

GLY356

2.831

ALA357

3.077

TYR360

3.642

PRO362

3.233

LEU370

4.724

ARG372

4.528

ARG373

3.206

GLU389

4.778

TYR391

4.340

ASP392

1.331

LEU394

1.330

SER395

3.630

PRO410

4.542

GLN411

3.038

Residue

Distance (Å)

PRO412

3.942

ALA413

3.032

PHE414

1.328

GLN416

1.325

LEU417

3.166

VAL418

3.197

ARG419

2.662

GLN420

3.444

PHE439

3.328

GLN447

2.744

ILE474

3.462

VAL475

4.697

VAL484

4.604

ARG485

4.637

ALA486

1.328

VAL488

1.329

GLY489

4.051

ASN499

2.765

ARG500

3.127

ALA501

1.328

GLN503

1.332

ALA504

3.644

ALA512

4.029

LYS513

3.290

PRO514

4.788

TYR517

4.098

LEU529

4.043

ASN530

3.686

THR531

3.427

TRP532

3.347

ILE533

4.730

ASP535

3.746

LEU540

4.196

ASN552

4.003

SER558

4.605

ARG562

4.631

VAL563

1.328

LEU565

1.336

VAL566

3.114

ASP567

2.986

ALA568

2.630

LEU569

4.838

ARG571

3.441

SER572

1.329

ASN574

1.329

VAL575

3.903

PRO576

3.475

THR577

2.767

VAL578

2.773

ASN579

3.697

LEU580

2.976

GLY581

1.321

ALA583

1.324

LEU584

3.194

GLY585

3.451

LEU586

3.399

VAL589

3.832

THR590

3.580

TRP593

4.408

LEU603

4.725

HIS604

3.646

PRO605

4.078

VAL606

3.171

PRO607

2.880

ALA608

1.324

LEU610

1.328

LEU611

3.074

GLY612

2.811

ALA613

3.365

LEU614

4.815

THR617

3.471

PRO618

4.920

ILE619

4.138

PHE625

3.770

ILE628

4.821

LEU669

4.811

THR670

2.728

LEU671

2.641

TRP672

3.349

THR673

1.327

GLN675

1.323

GLN676

2.964

VAL677

2.739

VAL678

3.027

THR682

4.216

GLY683

2.987

ARG684

4.020

GLN685

3.242

LEU686

3.290

LEU695

4.462

ALA696

3.878

GLY697

3.334

LYS698

3.403

THR699

4.138

PHE710

3.564

ALA711

4.742

ILE713

4.835

ALA736

3.016

SER737

3.766

GLY738

3.054

ALA739

1.325

SER741

1.327

ILE742

3.384

TYR743

3.700

GLN744

2.966

ALA764

3.228

ASP765

1.329

GLY767

1.321

VAL768

3.249

ASP769

3.604

TYR770

3.953

ASP771

4.338

GLY772

3.064

PHE774

3.977

GLY778

4.543

GLY779

1.326

ARG781

1.321

ILE782

3.241

LEU783

2.804

PRO784

4.965

VAL785

3.576

THR787

4.558

PRO790

3.725

SER792

4.485

LEU793

3.414

GLN795

3.698

GLN796

3.738

SER797

4.318

GLU798

1.330

Click to View More Binding Site Information of This Target with Different Ligands

Different Human System Profiles of Target	Top
Human Similarity Proteins of target is determined by comparing the sequence similarity of all human proteins with the target based on BLAST. The similarity proteins for a target are defined as the proteins with E-value < 0.005 and outside the protein families of the target. A target that has fewer human similarity proteins outside its family is commonly regarded to possess a greater capacity to avoid undesired interactions and thus increase the possibility of finding successful drugs (Brief Bioinform, 21: 649-662, 2020). Human Similarity Proteins

Different Human System Profiles of Target

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Human Similarity Proteins of target is determined by comparing the sequence similarity of all human proteins with the target based on BLAST. The similarity proteins for a target are defined as the proteins with E-value < 0.005 and outside the protein families of the target.

A target that has fewer human similarity proteins outside its family is commonly regarded to possess a greater capacity to avoid undesired interactions and thus increase the possibility of finding successful drugs (Brief Bioinform, 21: 649-662, 2020).

Human Similarity Proteins

There is no similarity protein (E value < 0.005) for this target

Chemical Structure based Activity Landscape of Target

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Target Poor or Non Binders

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Target Poor or Non Binders

Target Poor or Non Binders Info

References

Top

REF 1

The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42.

REF 2

DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res. 2011 Jan;39(Database issue):D1035-41.

REF 3

Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli. Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8824-9.

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