Protein profile

KP13_06703

Carbepenem-hydrolyzing beta-lactamase KPC2

Genome: KpKP13

Gene: AHE41807.1 Structure source: Experimental + ColabFold UniProt Q9F663
Amino acids 293
Annotations 6
Features 31
PDB binders 36
Druggability 0.994

Overview

Basic information about this protein and its source genome.

Accession
KP13_06703
Gene
AHE41807.1
Status
annotated
Amino acids
293
Structure source
Experimental + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Unknown
ColabFold pLDDT
92.9

Selected Druggability evidence

PDB experimental structure

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.994
Structure 6JN4
Pocket Pocket 1
P2Rank 0.71
Structure 6Z25
Pocket Pocket 1
ColabFold model
FPocket 0.609 · Pocket 2
P2Rank 0.429 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 35 / 4744 genomes with a hit
Normalized 0.007

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0008800 Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
  • GO:0017001 The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
  • GO:0030655 The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
24 286 PANTHER PTHR35333 BETA-LACTAMASE
24 286 InterPro IPR000871 Beta-lactamase, class-A
24 293 Gene3D G3DSA:3.40.710.10 -
24 293 InterPro IPR012338 Beta-lactamase/transpeptidase-like
1 24 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
29 287 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
29 287 InterPro IPR012338 Beta-lactamase/transpeptidase-like
1 19 SignalP_EUK SignalP-noTM SignalP-noTM
27 293 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
19 26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
141 165 PRINTS PR00118 Beta-lactamase class A signature
141 165 InterPro IPR000871 Beta-lactamase, class-A
32 56 PRINTS PR00118 Beta-lactamase class A signature
32 56 InterPro IPR000871 Beta-lactamase, class-A
105 130 PRINTS PR00118 Beta-lactamase class A signature
105 130 InterPro IPR000871 Beta-lactamase, class-A
63 80 PRINTS PR00118 Beta-lactamase class A signature
63 80 InterPro IPR000871 Beta-lactamase, class-A
203 218 PRINTS PR00118 Beta-lactamase class A signature
203 218 InterPro IPR000871 Beta-lactamase, class-A
167 192 PRINTS PR00118 Beta-lactamase class A signature
167 192 InterPro IPR000871 Beta-lactamase, class-A
220 235 PRINTS PR00118 Beta-lactamase class A signature
220 235 InterPro IPR000871 Beta-lactamase, class-A
45 263 Pfam PF13354 Beta-lactamase enzyme family
45 263 InterPro IPR045155 Beta-lactamase class A, catalytic domain
1 26 Phobius SIGNAL_PEPTIDE Signal peptide region
7 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 24 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

Loading 3D structure...

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Structural evidence

78 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 6TD0
X-ray 0.99 Å A
91.8% 25-293
Viewing
PDB 7TB7
X-ray 0.99 Å A
90.8% 24-289
Loaded
PDB 6QW9
X-ray 1.04 Å A
91.8% 25-293
Loaded
PDB 6QWB
X-ray 1.04 Å A
91.8% 25-293
Loaded
PDB 8RWQ
X-ray 1.05 Å A
91.8% 25-293
Loaded
PDB 6QWA
X-ray 1.06 Å A
91.8% 25-293
Loaded
PDB 8RWS
X-ray 1.09 Å A
91.8% 25-293
Loaded
PDB 9F0U
X-ray 1.11 Å A
91.8% 25-293
Loaded
PDB 8RWO
X-ray 1.13 Å A
91.8% 25-293
Loaded
PDB 5UL8
X-ray 1.15 Å A
91.8% 25-293
Loaded
PDB 7TC1
X-ray 1.16 Å A
90.8% 24-289
Loaded
PDB 6XD5
X-ray 1.20 Å A
100.0% 1-293
Loaded
PDB 6QWD
X-ray 1.20 Å A
91.8% 25-293
Loaded
PDB 6TD1
X-ray 1.20 Å A
91.8% 25-293
Loaded
PDB 6Z25
X-ray 1.24 Å A
91.8% 25-293
Loaded
PDB 6V7I
X-ray 1.25 Å A
91.8% 25-293
Loaded
PDB 6Z24
X-ray 1.25 Å A
91.8% 25-293
Loaded
PDB 7A61
X-ray 1.25 Å A
91.8% 25-293
Loaded
PDB 8G2T
X-ray 1.26 Å A
90.8% 24-289
Loaded
PDB 3RXW
X-ray 1.26 Å A
90.1% 26-289
Loaded
PDB 8G2R
X-ray 1.28 Å A
90.8% 24-289
Loaded
PDB 6D15
X-ray 1.30 Å A
91.8% 25-293
Loaded
PDB 6QWC
X-ray 1.30 Å A
91.8% 25-293
Loaded
PDB 6V1J
X-ray 1.30 Å A
91.8% 25-293
Loaded
PDB 6Z21
X-ray 1.30 Å A
91.8% 25-293
Loaded
PDB 6Z23
X-ray 1.31 Å A
91.8% 25-293
Loaded
PDB 6D18
X-ray 1.35 Å A
91.8% 25-293
Loaded
PDB 8AKJ
X-ray 1.35 Å A
91.8% 25-293
Loaded
PDB 8AKL
X-ray 1.35 Å A
91.8% 25-293
Loaded
PDB 8AKK
X-ray 1.36 Å A
91.8% 25-293
Loaded
PDB 7UTB
X-ray 1.38 Å A
90.8% 24-289
Loaded
PDB 5UJ4
X-ray 1.40 Å A
91.8% 25-293
Loaded
PDB 6D16
X-ray 1.40 Å A
91.8% 25-293
Loaded
PDB 6QWE
X-ray 1.40 Å A
91.8% 25-293
Loaded
PDB 6Z22
X-ray 1.40 Å A
91.8% 25-293
Loaded
PDB 8AKI
X-ray 1.40 Å A
91.8% 25-293
Loaded
PDB 6MEY
X-ray 1.42 Å A
91.8% 25-293
Loaded
PDB 7LK8
X-ray 1.43 Å A,B
88.7% 30-289
Loaded
PDB 6B1F
X-ray 1.44 Å A,B
91.5% 22-289
Loaded
PDB 5UJ3
X-ray 1.45 Å A
91.8% 25-293
Loaded
PDB 6D17
X-ray 1.45 Å A
91.8% 25-293
Loaded
PDB 6D19
X-ray 1.45 Å A
91.8% 25-293
Loaded
PDB 6B1X
X-ray 1.45 Å A,B
91.5% 22-289
Loaded
PDB 7LR9
X-ray 1.47 Å A,B
91.5% 22-289
Loaded
PDB 6B1J
X-ray 1.60 Å A,B
91.5% 22-289
Loaded
PDB 7U8S
X-ray 1.60 Å A
90.4% 26-290
Loaded
PDB 3RXX
X-ray 1.62 Å A
90.1% 26-289
Loaded
PDB 6XD7
X-ray 1.65 Å A
100.0% 1-293
Loaded
PDB 7LLB
X-ray 1.67 Å A,B
90.1% 26-289
Loaded
PDB 6M7I
X-ray 1.70 Å A
91.8% 25-293
Loaded
PDB 6B1W
X-ray 1.73 Å A,B
91.5% 22-289
Loaded
PDB 7TI2
X-ray 1.75 Å A
91.8% 25-293
Loaded
PDB 6J8Q
X-ray 1.79 Å A,B,C,D
90.1% 26-289
Loaded
PDB 6B1H
X-ray 1.80 Å A,B
91.5% 22-289
Loaded
PDB 6B1Y
X-ray 1.80 Å A,B
91.5% 22-289
Loaded
PDB 4ZBE
X-ray 1.80 Å A
90.1% 26-289
Loaded
PDB 7LJK
X-ray 1.81 Å A,B
90.1% 26-289
Loaded
PDB 7LNL
X-ray 1.82 Å A,B
91.5% 22-289
Loaded
PDB 2OV5
X-ray 1.85 Å A,B,C
89.1% 30-290
Loaded
PDB 6MLL
X-ray 1.86 Å A
91.8% 25-293
Loaded
PDB 5EEC
X-ray 1.87 Å A,B
91.8% 25-293
Loaded
PDB 3E2L
X-ray 1.87 Å A,B
90.1% 30-293
Loaded
PDB 6JN4
X-ray 1.90 Å A,B,C,D
90.1% 26-289
Loaded
PDB 7U9B
X-ray 1.95 Å A
91.1% 25-291
Loaded
PDB 6JN5
X-ray 1.97 Å A,B,C,D
90.1% 26-289
Loaded
PDB 6XJ8
X-ray 2.05 Å A
100.0% 1-293
Loaded
PDB 3E2K
X-ray 2.10 Å A,B
90.1% 30-293
Loaded
PDB 7LLH
X-ray 2.10 Å A,B
88.7% 29-288
Loaded
PDB 6MNP
X-ray 2.20 Å A
91.8% 25-293
Loaded
PDB 6JN3
X-ray 2.22 Å A,B,C,D
90.1% 26-289
Loaded
PDB 7UA7
X-ray 2.25 Å A
91.5% 25-292
Loaded
PDB 7E9A
X-ray 2.25 Å A,B,C,D
90.1% 26-289
Loaded
PDB 7VQN
X-ray 2.34 Å A,B,C,D
90.4% 25-289
Loaded
PDB 7TBX
X-ray 3.16 Å A,B
91.1% 23-289
Loaded
PDB 8RWR
X-ray 1.03 Å A
91.8% 25-293
PDB 9FBT
X-ray 1.07 Å A
91.8% 25-293
PDB 8RWP
X-ray 1.19 Å A
91.8% 25-293
PDB 8AKM
X-ray 1.25 Å A
91.8% 25-293
ColabFold KP13_06703
ColabFold full sequence Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.816

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 10.67 0.573

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

186 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
1CE 288.3 Da LogP 0.90 TPSA 89.4 ✓ Ro5 ✓ Clean C1CCc2c(c3c(s2)N=CN(C3=O)Cc4[nH]nnn4)C1
8YF 317.4 Da LogP -0.34 TPSA 142.7 1 viol. ✓ Clean [H]/N=C/NCCSC1=C(N[C@H](C1)[C@@H]([C@@H](C)O)C(…
BHU 177.0 Da LogP -1.32 TPSA 69.6 ✓ Ro5 ✓ Clean B(CNC(=O)[C@H](C)CS)(O)O
BX6 267.2 Da LogP 0.29 TPSA 69.6 ✓ Ro5 ✓ Clean B([C@H](Cc1ccccc1)NC(=O)[C@H](C)CS)(O)O
BX9 271.1 Da LogP 0.56 TPSA 69.6 ✓ Ro5 ✓ Clean B([C@H](c1ccc(cc1)F)NC(=O)[C@H](C)CS)(O)O
BXU 271.1 Da LogP 0.56 TPSA 69.6 ✓ Ro5 ✓ Clean B([C@@H](c1ccc(cc1)F)NC(=O)[C@H](C)CS)(O)O
C8V 393.4 Da LogP -2.55 TPSA 166.2 ✓ Ro5 ✓ Clean C1C[C@H](CNC1)C(=O)NNC(=O)[C@@H]2CC[C@H](CN2C=O…
C8Y 249.2 Da LogP -1.18 TPSA 119.7 ✓ Ro5 ✓ Clean C1CC(N(CC1NOS(=O)(=O)O)C=O)C#N
C9D 379.4 Da LogP -2.94 TPSA 166.2 ✓ Ro5 ✓ Clean C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)NNC(=O…
CAZ 469.5 Da LogP 0.15 TPSA 193.6 1 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
CD7 377.4 Da LogP -2.17 TPSA 169.2 ✓ Ro5 ✓ Clean [H]/N=C\1/CC[C@H](N(C1)C=O)C(=O)NNC(=O)[C@@H]2C…
CE4 413.4 Da LogP -0.20 TPSA 176.6 ✓ Ro5 ✓ Clean CO/N=C(/c1csc(n1)N)\C(=O)N[C@@H]([C@@H]2N=C(C(=…
CEF 397.4 Da LogP -0.09 TPSA 156.3 ✓ Ro5 ✓ Clean CO/N=C(/c1csc(n1)N)\C(=O)NC(C=O)C2N=C(C(=C)CS2)…
FUJ 270.2 Da LogP 1.48 TPSA 97.0 ✓ Ro5 ✓ Clean COc1ccc2c(c1)OC(=O)C=C2CP(=O)(O)O
GTV 268.2 Da LogP 2.09 TPSA 87.7 ✓ Ro5 ✓ Clean Cc1cc(c2c(c1)OC(=O)C=C2CP(=O)(O)O)C
J84 296.1 Da LogP 1.94 TPSA 98.3 ✓ Ro5 ✓ Clean c1cc(c(cc1Cl)Cl)n2c(c(cn2)c3[nH]nnn3)N
JJT 268.3 Da LogP 0.02 TPSA 105.5 ✓ Ro5 ✓ Clean C1CC(=N)CN([C@@H]1C(=O)NC2CCNCC2)C(=O)O
KJK 389.3 Da LogP 0.32 TPSA 133.9 ✓ Ro5 ✓ Clean B1([C@H](Cc2cccc(c2O1)C(=O)O)NC(=O)CC3CCC(CC3)N…
MK7 350.4 Da LogP -1.83 TPSA 137.1 ✓ Ro5 ✓ Clean C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)NC2CCN…
N1G 331.3 Da LogP 2.30 TPSA 101.4 ✓ Ro5 ✓ Clean c1ccc(cc1)c2cc(nn2c3ccccc3)C(=O)Nc4[nH]nnn4
NPB 166.9 Da LogP -0.73 TPSA 83.6 ✓ Ro5 ✓ Clean B(c1cccc(c1)[N+](=O)[O-])(O)O
NXL 267.3 Da LogP -2.21 TPSA 139.0 ✓ Ro5 ✓ Clean C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)N
O5E 294.3 Da LogP 1.99 TPSA 95.6 ✓ Ro5 ✓ Clean c1ccc(cc1)[C@H](C(=O)Nc2[nH]nnn2)Nc3ccccc3
QNA 239.0 Da LogP 0.70 TPSA 87.0 ✓ Ro5 ✓ Clean [B-]1([C@@H]2C[C@@H]2c3ccc(c(c3O1)C(=O)O)F)(O)O
RM9 222.0 Da LogP 1.25 TPSA 66.8 ✓ Ro5 ✓ Clean B1([C@@H]2C[C@@H]2c3ccc(c(c3O1)C(=O)O)F)O
SFR 303.3 Da LogP 0.21 TPSA 116.1 ✓ Ro5 ✓ Clean C[C@H]([C@H]([C@@H]1NC(=C(S1)[C@H]2CCCO2)C(=O)O…
SR3 324.3 Da LogP -1.52 TPSA 176.2 1 viol. ✓ Clean C[C@@]([C@H](C(=O)O)N/C=C/C=O)(C(=O)OCC(=O)N)S(…
TWB 268.2 Da LogP 2.09 TPSA 87.7 ✓ Ro5 ✓ Clean Cc1cc2c(cc1C)OC(=O)C=C2CP(=O)(O)O
VKE 284.2 Da LogP 1.20 TPSA 106.2 ✓ Ro5 ✓ Clean c1c2c(cc3c1OCO3)OC(=O)C=C2CP(=O)(O)O
YKG 333.1 Da LogP 2.54 TPSA 87.7 ✓ Ro5 ✓ Clean Cc1cc2c(c(c1)Br)C(=CC(=O)O2)CP(=O)(O)O
ZXM 324.1 Da LogP -1.22 TPSA 137.6 ✓ Ro5 ✓ Clean B([C@H](Cn1cc(nn1)C(=O)O)NC(=O)Cc2cccs2)(O)O
ZZ7 367.4 Da LogP 0.15 TPSA 141.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)[C@@H]…

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.