Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T10

L. infantum R5P L. infantum

Ligand MK27

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

54.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 1.00, Jaccard 0.94, H-bond role recall 0.64

Burial

61%

Hydrophobic fit

80%

Reason: strain 54.0 kcal/mol

strain ΔE 54.0 kcal/mol 4 protein-contact clashes 4 intramolecular clashes 74% of hydrophobic surface is solvent-exposed (20/27 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-0.401 kcal/mol/HA) ✓ Good fit quality (FQ -4.07) ✓ Strong H-bond network (7 bonds) ✓ Good burial (61% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (54.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)

Score

-14.417

kcal/mol

-0.401

kcal/mol/HA

Fit Quality

-4.07

FQ (Leeson)

HAC

heavy atoms

519

LogP

2.26

cLogP

Final rank

5.1022

rank score

Inter norm

-0.688

normalised

Contacts

H-bonds 13

Strain ΔE

54.0 kcal/mol

SASA buried

61%

Lipo contact

80% BSA apolar/total

SASA unbound

838 Å²

Apolar buried

408 Å²

Interaction summary

HBA 7 HY 3 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.

Name	6FXW	Contacts	17
Pose	Open native pose	HB	0
IFP residues	ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap	17	Native recall	1.00
Jaccard	0.94	RMSD	-
HB strict	7	Strict recall	0.54
HB same residue+role	7	HB role recall	0.64
HB same residue	8	HB residue recall	0.73

Protein summary

155 residues

Protein target	T10	Atoms	4590
Residues	155	Chains	1
Residue summary	ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
353	2.925637514091269	-0.674099	-21.9374	4	18	0	0.00	0.00	-	no	Open
284	3.7038824639745087	-0.628274	-19.3613	4	17	0	0.00	0.00	-	no	Open
188	5.102161794543185	-0.687821	-14.4168	13	18	17	1.00	0.64	-	no	Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -14.417kcal/mol

Ligand efficiency (LE) -0.4005kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -4.070

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 36HA

Physicochemical properties

Molecular weight 518.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.26

Lipinski: ≤ 5

Rotatable bonds 9

Conformational strain (MMFF94s)

Strain energy (ΔE) 54.01kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy 112.28kcal/mol

Minimised FF energy 58.27kcal/mol

SASA & burial

✓ computed

SASA (unbound) 837.9Å²

Total solvent-accessible surface area of free ligand

BSA total 513.8Å²

Buried surface area upon binding

BSA apolar 408.2Å²

Hydrophobic contacts buried

BSA polar 105.6Å²

Polar contacts buried

Fraction buried 61.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 79.5%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2460.7Å²

SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.

Receptor non-polar SASA 2417.4Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 677.6Å²

Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)