Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T05

L. major PTR1 L. major

Ligand Z56836330

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 but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

10.5 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.71, Jaccard 0.60, H-bond role recall 0.33

Burial

92%

Hydrophobic fit

81%

Reason: 9 internal clashes

9 intramolecular clashes

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 (-1.265 kcal/mol/HA) ✓ Good fit quality (FQ -10.79) ✓ Good H-bonds (5 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Moderate strain (10.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-26.571

kcal/mol

-1.265

kcal/mol/HA

Fit Quality

-10.79

FQ (Leeson)

HAC

heavy atoms

342

LogP

3.25

cLogP

Final rank

1.1201

rank score

Inter norm

-1.322

normalised

Contacts

H-bonds 7

Strain ΔE

10.5 kcal/mol

SASA buried

92%

Lipo contact

81% BSA apolar/total

SASA unbound

510 Å²

Apolar buried

382 Å²

Interaction summary

HBD 3 HBA 2 HY 6 PI 3 CLASH 0

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PI · π–π interactions

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

HY · Hydrophobic contacts

CLASH · Clashes

No clash · clashes detected for this pose.

Native ligand reference

★ reference

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

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	12	Native recall	0.71
Jaccard	0.60	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
377	1.1201034903288134	-1.32155	-26.5708	7	15	12	0.71	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 -26.571kcal/mol

Ligand efficiency (LE) -1.2653kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.792

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

Heavy atom count 21HA

Physicochemical properties

Molecular weight 342.2Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.25

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 10.46kcal/mol

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

Docked FF energy 40.03kcal/mol

Minimised FF energy 29.57kcal/mol

SASA & burial

✓ computed

SASA (unbound) 509.5Å²

Total solvent-accessible surface area of free ligand

BSA total 471.0Å²

Buried surface area upon binding

BSA apolar 381.6Å²

Hydrophobic contacts buried

BSA polar 89.5Å²

Polar contacts buried

Fraction buried 92.4%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 81.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1561.1Å²

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 1037.9Å²

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