Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T05

L. major PTR1 L. major

Ligand Z266761848

PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Promising SASA cached

Promising and worth follow-up

Binding strong Geometry medium Native strong SASA done

Strain ΔE

13.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.59, Jaccard 0.48, H-bond role recall 0.33

Burial

85%

Hydrophobic fit

84%

Reason: no major geometry red flags detected

4 protein-contact clashes 4 intramolecular clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-0.973 kcal/mol/HA) ✓ Good fit quality (FQ -8.72) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (13.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-23.347

kcal/mol

-0.973

kcal/mol/HA

Fit Quality

-8.72

FQ (Leeson)

HAC

heavy atoms

343

LogP

3.53

cLogP

Final rank

1.8008

rank score

Inter norm

-1.179

normalised

Contacts

H-bonds 2

Strain ΔE

13.2 kcal/mol

SASA buried

85%

Lipo contact

84% BSA apolar/total

SASA unbound

601 Å²

Apolar buried

431 Å²

Interaction summary

HBD 1 HBA 1 HY 5 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.

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	ligand	Contacts	17
Pose	Open native pose	HB	0
IFP residues	ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap	10	Native recall	0.59
Jaccard	0.48	RMSD	-
HB strict	2	Strict recall	0.29
HB same residue+role	2	HB role recall	0.33
HB same residue	2	HB residue recall	0.40

Protein summary

274 residues

Protein target	T05	Atoms	4108
Residues	274	Chains	2
Residue summary	LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:NDP302

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
426	1.8008473567312993	-1.1791	-23.3472	2	14	10	0.59	0.33	-	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 -23.347kcal/mol

Ligand efficiency (LE) -0.9728kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.718

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

Heavy atom count 24HA

Physicochemical properties

Molecular weight 342.8Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.53

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 13.17kcal/mol

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

Docked FF energy 25.23kcal/mol

Minimised FF energy 12.05kcal/mol

SASA & burial

✓ computed

SASA (unbound) 601.5Å²

Total solvent-accessible surface area of free ligand

BSA total 510.0Å²

Buried surface area upon binding

BSA apolar 430.6Å²

Hydrophobic contacts buried

BSA polar 79.4Å²

Polar contacts buried

Fraction buried 84.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 84.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1636.2Å²

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 2179.4Å²

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

Complex non-polar SASA 1054.0Å²

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