Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T05

L. major PTR1 L. major

Ligand KB_Leish_22

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

15.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.53, Jaccard 0.39, H-bond role recall 0.17

Burial

98%

Hydrophobic fit

82%

Reason: no major geometry red flags detected

4 protein-contact clashes 5 intramolecular clashes

EcoTox / ADMET GDS: SAFE UL GreenDrugScore ML model

ECOscore

0.282

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.402

ADMET + ECO + DL

ADMETscore (GDS)

0.417

absorption · distr. · metab.

DLscore

0.447

drug-likeness

P(SAFE)

0.59

GDS classification

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-1.501 kcal/mol/HA) ✓ Good fit quality (FQ -12.30) ✓ Good H-bonds (4 bonds) ✓ Deep burial (98% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (15.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-28.516

kcal/mol

-1.501

kcal/mol/HA

Fit Quality

-12.30

FQ (Leeson)

HAC

heavy atoms

268

LogP

3.65

cLogP

Final rank

1.9979

rank score

Inter norm

-1.473

normalised

Contacts

H-bonds 4

Strain ΔE

15.2 kcal/mol

SASA buried

98%

Lipo contact

82% BSA apolar/total

SASA unbound

505 Å²

Apolar buried

406 Å²

Interaction summary

HBA 4 HY 7 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	9	Native recall	0.53
Jaccard	0.39	RMSD	-
HB strict	1	Strict recall	0.14
HB same residue+role	1	HB role recall	0.17
HB same residue	1	HB residue recall	0.20

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
93	1.9979261671881465	-1.47339	-28.5161	4	15	9	0.53	0.17	-	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 -28.516kcal/mol

Ligand efficiency (LE) -1.5008kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -12.302

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

Heavy atom count 19HA

Physicochemical properties

Molecular weight 268.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.65

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 15.19kcal/mol

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

Docked FF energy 15.46kcal/mol

Minimised FF energy 0.27kcal/mol

SASA & burial

✓ computed

SASA (unbound) 505.3Å²

Total solvent-accessible surface area of free ligand

BSA total 495.0Å²

Buried surface area upon binding

BSA apolar 406.2Å²

Hydrophobic contacts buried

BSA polar 88.8Å²

Polar contacts buried

Fraction buried 98.0%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 82.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1568.8Å²

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 1026.7Å²

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