Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T04

L. major PTR1 L. major

Ligand ulfkktlib_1190

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 high Native strong SASA done

Strain ΔE

1.8 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.32, Jaccard 0.32, H-bond role recall 0.60

Burial

93%

Hydrophobic fit

77%

Reason: no major geometry red flags detected

EcoTox / ADMET GDS: SAFE UL GreenDrugScore ML model

ECOscore

0.902

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.590

ADMET + ECO + DL

ADMETscore (GDS)

0.590

absorption · distr. · metab.

DLscore

0.403

drug-likeness

P(SAFE)

0.52

GDS classification

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Low conformational strain (1.8 kcal/mol) ✓ Excellent LE (-2.997 kcal/mol/HA) ✓ Good fit quality (FQ -15.71) ✓ Good H-bonds (4 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Geometry warnings

Score

-23.977

kcal/mol

-2.997

kcal/mol/HA

Fit Quality

-15.71

FQ (Leeson)

HAC

heavy atoms

109

LogP

0.37

cLogP

Final rank

-1.0173

rank score

Inter norm

-2.997

normalised

Contacts

H-bonds 5

Strain ΔE

1.8 kcal/mol

SASA buried

93%

Lipo contact

77% BSA apolar/total

SASA unbound

285 Å²

Apolar buried

205 Å²

Interaction summary

HBD 2 HBA 2 HY 1 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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	7PXX	Contacts	19
Pose	Open native pose	HB	0
IFP residues	ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap	6	Native recall	0.32
Jaccard	0.32	RMSD	-
HB strict	4	Strict recall	0.67
HB same residue+role	3	HB role recall	0.60
HB same residue	3	HB residue recall	0.60

Protein summary

308 residues

Protein target	T04	Atoms	4210
Residues	308	Chains	3
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
117	-1.0173221485750368	-2.99711	-23.9769	5	6	6	0.32	0.60	-	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 -23.977kcal/mol

Ligand efficiency (LE) -2.9971kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -15.712

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

Heavy atom count 8HA

Physicochemical properties

Molecular weight 109.1Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.37

Lipinski: ≤ 5

Rotatable bonds 1

Conformational strain (MMFF94s)

Strain energy (ΔE) 1.77kcal/mol

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

Docked FF energy 4.88kcal/mol

Minimised FF energy 3.12kcal/mol

SASA & burial

✓ computed

SASA (unbound) 284.9Å²

Total solvent-accessible surface area of free ligand

BSA total 264.5Å²

Buried surface area upon binding

BSA apolar 204.6Å²

Hydrophobic contacts buried

BSA polar 59.9Å²

Polar contacts buried

Fraction buried 92.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 77.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1377.1Å²

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 1027.3Å²

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