Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T05

L. major PTR1 L. major

Ligand Z19474712

PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Likely artefact or unreliable pose

Binding strong Geometry medium Native strong SASA done

Strain ΔE

31.8 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.65, Jaccard 0.48, H-bond role recall 0.33

Burial

79%

Hydrophobic fit

79%

Reason: no major geometry red flags detected

5 protein-contact clashes 5 intramolecular clashes

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.282

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.380

ADMET + ECO + DL

ADMETscore (GDS)

0.381

absorption · distr. · metab.

DLscore

0.437

drug-likeness

P(SAFE)

0.38

GDS classification

ADMET alerts (in-silico)

hERG High Ames Clear DILI Risk

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-0.959 kcal/mol/HA) ✓ Good fit quality (FQ -9.51) ✓ Good H-bonds (3 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (31.8 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (8) ✗ Many internal clashes (11)

Score

-31.638

kcal/mol

-0.959

kcal/mol/HA

Fit Quality

-9.51

FQ (Leeson)

HAC

heavy atoms

500

LogP

5.41

cLogP

Final rank

1.7582

rank score

Inter norm

-0.874

normalised

Contacts

H-bonds 4

Strain ΔE

31.8 kcal/mol

SASA buried

79%

Lipo contact

79% BSA apolar/total

SASA unbound

714 Å²

Apolar buried

447 Å²

Interaction summary

HBA 3 HY 8 PI 2 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	11	Native recall	0.65
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
582	1.7581735256716562	-0.874492	-31.6378	4	17	11	0.65	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 -31.638kcal/mol

Ligand efficiency (LE) -0.9587kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.512

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

Heavy atom count 33HA

Physicochemical properties

Molecular weight 499.9Da

Lipinski: ≤ 500 Da

LogP (cLogP) 5.41

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 31.83kcal/mol

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

Docked FF energy 20.63kcal/mol

Minimised FF energy -11.20kcal/mol

SASA & burial

✓ computed

SASA (unbound) 714.4Å²

Total solvent-accessible surface area of free ligand

BSA total 564.2Å²

Buried surface area upon binding

BSA apolar 447.4Å²

Hydrophobic contacts buried

BSA polar 116.9Å²

Polar contacts buried

Fraction buried 79.0%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 79.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1726.3Å²

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 1040.8Å²

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