Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T05

L. major PTR1 L. major

Ligand Z20272268

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 mixed SASA done

Strain ΔE

10.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.53, Jaccard 0.45, H-bond role recall 0.33

Burial

86%

Hydrophobic fit

64%

Reason: no major geometry red flags detected

3 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 (-1.317 kcal/mol/HA) ✓ Good fit quality (FQ -11.23) ✓ Good H-bonds (5 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ Moderate strain (10.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)

Score

-27.649

kcal/mol

-1.317

kcal/mol/HA

Fit Quality

-11.23

FQ (Leeson)

HAC

heavy atoms

321

LogP

3.31

cLogP

Final rank

1.2449

rank score

Inter norm

-1.371

normalised

Contacts

H-bonds 6

Strain ΔE

10.2 kcal/mol

SASA buried

86%

Lipo contact

64% BSA apolar/total

SASA unbound

547 Å²

Apolar buried

302 Å²

Interaction summary

HBA 5 HY 5 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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	9	Native recall	0.53
Jaccard	0.45	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
427	1.2448782996832295	-1.37087	-27.649	6	12	9	0.53	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 -27.649kcal/mol

Ligand efficiency (LE) -1.3166kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -11.230

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

Heavy atom count 21HA

Physicochemical properties

Molecular weight 321.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.31

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 10.17kcal/mol

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

Docked FF energy 13.29kcal/mol

Minimised FF energy 3.12kcal/mol

SASA & burial

✓ computed

SASA (unbound) 546.7Å²

Total solvent-accessible surface area of free ligand

BSA total 469.0Å²

Buried surface area upon binding

BSA apolar 301.9Å²

Hydrophobic contacts buried

BSA polar 167.2Å²

Polar contacts buried

Fraction buried 85.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 64.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1520.1Å²

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 1032.2Å²

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