Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T04

L. major PTR1 L. major

Ligand OHD_TB2022_3

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

17.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.58, Jaccard 0.58, H-bond role recall 0.20

Burial

86%

Hydrophobic fit

77%

Reason: no major geometry red flags detected

1 protein-contact 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)

0.384

absorption · distr. · metab.

DLscore

0.433

drug-likeness

GDS₂ (2-block)

0.358

ECO + ADMET

P(SAFE)

8.9%

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 (-1.040 kcal/mol/HA) ✓ Good fit quality (FQ -8.87) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Moderate strain (17.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-21.834

kcal/mol

-1.040

kcal/mol/HA

Fit Quality

-8.87

FQ (Leeson)

HAC

heavy atoms

298

LogP

3.29

cLogP

Final rank

2.2201

rank score

Inter norm

-1.160

normalised

Contacts

H-bonds 2

Strain ΔE

17.7 kcal/mol

SASA buried

86%

Lipo contact

77% BSA apolar/total

SASA unbound

525 Å²

Apolar buried

349 Å²

Interaction summary

HBA 2 HY 6 PI 4 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

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	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	11	Native recall	0.58
Jaccard	0.58	RMSD	-
HB strict	1	Strict recall	0.17
HB same residue+role	1	HB role recall	0.20
HB same residue	1	HB residue recall	0.20

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
35	2.2201235527984613	-1.15967	-21.8342	2	11	11	0.58	0.20	-	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 -21.834kcal/mol

Ligand efficiency (LE) -1.0397kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.868

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

Heavy atom count 21HA

Physicochemical properties

Molecular weight 298.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.29

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 17.70kcal/mol

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

Docked FF energy 43.42kcal/mol

Minimised FF energy 25.72kcal/mol

SASA & burial

✓ computed

SASA (unbound) 524.9Å²

Total solvent-accessible surface area of free ligand

BSA total 454.1Å²

Buried surface area upon binding

BSA apolar 349.4Å²

Hydrophobic contacts buried

BSA polar 104.7Å²

Polar contacts buried

Fraction buried 86.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 76.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1551.7Å²

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 1027.7Å²

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