Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T05

L. major PTR1 L. major

Ligand Z266766336

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

15.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.59, Jaccard 0.53, H-bond role recall 0.33

Burial

88%

Hydrophobic fit

84%

Reason: no major geometry red flags detected

2 protein-contact clashes 4 intramolecular clashes 47% of hydrophobic surface appears solvent-exposed (8/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Algae IC₅₀

Cat. 3 — Harmful (10–100 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 (-0.995 kcal/mol/HA) ✓ Good fit quality (FQ -8.78) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (15.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-22.880

kcal/mol

-0.995

kcal/mol/HA

Fit Quality

-8.78

FQ (Leeson)

HAC

heavy atoms

308

LogP

2.88

cLogP

Final rank

1.5279

rank score

Inter norm

-1.235

normalised

Contacts

H-bonds 2

Strain ΔE

15.7 kcal/mol

SASA buried

88%

Lipo contact

84% BSA apolar/total

SASA unbound

571 Å²

Apolar buried

420 Å²

Interaction summary

HBD 1 HBA 1 HY 4 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	0.53	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
378	1.5279176286492464	-1.23504	-22.8798	2	12	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 -22.880kcal/mol

Ligand efficiency (LE) -0.9948kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.780

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

Heavy atom count 23HA

Physicochemical properties

Molecular weight 308.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.88

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 15.70kcal/mol

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

Docked FF energy 27.92kcal/mol

Minimised FF energy 12.22kcal/mol

SASA & burial

✓ computed

SASA (unbound) 571.4Å²

Total solvent-accessible surface area of free ligand

BSA total 500.8Å²

Buried surface area upon binding

BSA apolar 420.3Å²

Hydrophobic contacts buried

BSA polar 80.4Å²

Polar contacts buried

Fraction buried 87.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 83.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1614.6Å²

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 1045.8Å²

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