Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T05

L. major PTR1 L. major

Ligand Z29461229

PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Weak or marginal quality

Binding strong Geometry medium Native mixed SASA done

Strain ΔE

32.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.35, Jaccard 0.26, H-bond role recall 0.33

Burial

98%

Hydrophobic fit

75%

Reason: no major geometry red flags detected

5 protein-contact clashes 5 intramolecular clashes 46% of hydrophobic surface appears solvent-exposed (6/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 2 — Toxic (1–10 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 Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-1.506 kcal/mol/HA) ✓ Good fit quality (FQ -12.35) ✓ Good H-bonds (4 bonds) ✓ Deep burial (98% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Very high strain energy (32.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)

Score

-28.622

kcal/mol

-1.506

kcal/mol/HA

Fit Quality

-12.35

FQ (Leeson)

HAC

heavy atoms

271

LogP

3.43

cLogP

Final rank

3.4855

rank score

Inter norm

-1.531

normalised

Contacts

H-bonds 6

Strain ΔE

32.0 kcal/mol

SASA buried

98%

Lipo contact

75% BSA apolar/total

SASA unbound

479 Å²

Apolar buried

350 Å²

Interaction summary

HBA 4 HY 5 PI 3 CLASH 5

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	6	Native recall	0.35
Jaccard	0.26	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
648	3.4854999105190023	-1.53135	-28.6215	6	12	6	0.35	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 -28.622kcal/mol

Ligand efficiency (LE) -1.5064kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -12.347

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

Heavy atom count 19HA

Physicochemical properties

Molecular weight 271.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.43

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 31.97kcal/mol

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

Docked FF energy 38.50kcal/mol

Minimised FF energy 6.53kcal/mol

SASA & burial

✓ computed

SASA (unbound) 478.8Å²

Total solvent-accessible surface area of free ligand

BSA total 467.5Å²

Buried surface area upon binding

BSA apolar 350.4Å²

Hydrophobic contacts buried

BSA polar 117.1Å²

Polar contacts buried

Fraction buried 97.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 75.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1515.6Å²

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 1024.3Å²

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