Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T21

T. cruzi R5P T. cruzi

Ligand OHD_TB2020_53

PDB3K7O↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

59.5 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 1.00, Jaccard 0.74, H-bond role recall 0.33

Burial

68%

Hydrophobic fit

90%

Reason: strain 59.5 kcal/mol

strain ΔE 59.5 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 39% of hydrophobic surface appears solvent-exposed (11/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

Yes

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.680 kcal/mol/HA) ✓ Good fit quality (FQ -7.05) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Extreme strain energy (59.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)

Score

-26.509

kcal/mol

-0.680

kcal/mol/HA

Fit Quality

-7.05

FQ (Leeson)

HAC

heavy atoms

539

LogP

1.19

cLogP

Final rank

5.5901

rank score

Inter norm

-0.643

normalised

Contacts

H-bonds 8

Strain ΔE

59.5 kcal/mol

SASA buried

68%

Lipo contact

90% BSA apolar/total

SASA unbound

732 Å²

Apolar buried

454 Å²

Interaction summary

HBD 2 HBA 5 HY 3 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

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	3K7O	Contacts	14
Pose	Open native pose	HB	0
IFP residues	ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap	14	Native recall	1.00
Jaccard	0.74	RMSD	-
HB strict	4	Strict recall	0.33
HB same residue+role	3	HB role recall	0.33
HB same residue	3	HB residue recall	0.38

Protein summary

305 residues

Protein target	T21	Atoms	4646
Residues	305	Chains	2
Residue summary	ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
31	5.5901206338666185	-0.642746	-26.5092	8	19	14	1.00	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 -26.509kcal/mol

Ligand efficiency (LE) -0.6797kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.054

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

Heavy atom count 39HA

Physicochemical properties

Molecular weight 538.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.19

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 59.50kcal/mol

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

Docked FF energy 265.95kcal/mol

Minimised FF energy 206.45kcal/mol

SASA & burial

✓ computed

SASA (unbound) 732.2Å²

Total solvent-accessible surface area of free ligand

BSA total 501.6Å²

Buried surface area upon binding

BSA apolar 454.1Å²

Hydrophobic contacts buried

BSA polar 47.5Å²

Polar contacts buried

Fraction buried 68.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 90.5%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2348.5Å²

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 2482.0Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 797.9Å²

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