Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T21

T. cruzi R5P T. cruzi

Ligand ulfkktlib_2028

PDB3K7O↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Weak or marginal quality

Binding strong Geometry high Native strong SASA done

Strain ΔE

21.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.93, Jaccard 0.72, H-bond role recall 0.56

Burial

72%

Hydrophobic fit

67%

Reason: no major geometry red flags detected

1 protein-contact clashes 39% of hydrophobic surface appears solvent-exposed (9/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.697

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.501

ADMET + ECO + DL

ADMETscore (GDS)

0.482

absorption · distr. · metab.

DLscore

0.418

drug-likeness

P(SAFE)

0.10

GDS classification

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-0.805 kcal/mol/HA) ✓ Good fit quality (FQ -7.92) ✓ Good H-bonds (5 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ High strain energy (21.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (21)

Score

-25.772

kcal/mol

-0.805

kcal/mol/HA

Fit Quality

-7.92

FQ (Leeson)

HAC

heavy atoms

432

LogP

2.69

cLogP

Final rank

4.5128

rank score

Inter norm

-0.841

normalised

Contacts

H-bonds 14

Strain ΔE

21.9 kcal/mol

SASA buried

72%

Lipo contact

67% BSA apolar/total

SASA unbound

675 Å²

Apolar buried

329 Å²

Interaction summary

HBD 1 HBA 4 HY 3 PI 4 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

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	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	13	Native recall	0.93
Jaccard	0.72	RMSD	-
HB strict	6	Strict recall	0.50
HB same residue+role	5	HB role recall	0.56
HB same residue	6	HB residue recall	0.75

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
218	4.340319573317319	-1.07131	-40.5655	14	22	0	0.00	0.00	-	no	Open
152	4.512812911117598	-0.840762	-25.7719	14	17	13	0.93	0.56	-	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 -25.772kcal/mol

Ligand efficiency (LE) -0.8054kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.920

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

Heavy atom count 32HA

Physicochemical properties

Molecular weight 432.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.69

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 21.95kcal/mol

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

Docked FF energy 98.01kcal/mol

Minimised FF energy 76.06kcal/mol

SASA & burial

✓ computed

SASA (unbound) 675.2Å²

Total solvent-accessible surface area of free ligand

BSA total 489.1Å²

Buried surface area upon binding

BSA apolar 328.8Å²

Hydrophobic contacts buried

BSA polar 160.3Å²

Polar contacts buried

Fraction buried 72.4%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 67.2%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2193.9Å²

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 762.4Å²

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