Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T02

Human DHFR Human

Ligand OSA_Lib_227

PDB5SD8↗

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 medium Native strong SASA done

Strain ΔE

39.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.76, Jaccard 0.64, H-bond role recall 0.00

Burial

92%

Hydrophobic fit

99%

Reason: no major geometry red flags detected

4 protein-contact clashes 4 intramolecular clashes

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

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 (-0.528 kcal/mol/HA) ✓ Good fit quality (FQ -5.37) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (99%) ✗ Very high strain energy (39.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)

Score

-19.005

kcal/mol

-0.528

kcal/mol/HA

Fit Quality

-5.37

FQ (Leeson)

HAC

heavy atoms

489

LogP

2.06

cLogP

Final rank

2.8221

rank score

Inter norm

-0.773

normalised

Contacts

H-bonds 1

Strain ΔE

39.0 kcal/mol

SASA buried

92%

Lipo contact

99% BSA apolar/total

SASA unbound

790 Å²

Apolar buried

722 Å²

Interaction summary

HBD 1 HY 13 PI 2 CLASH 4

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	5SD8	Contacts	21
Pose	Open native pose	HB	0
IFP residues	ALA10 ASN65 ASP22 GLN36 GLU31 GLY117 GLY21 ILE61 ILE8 LEU23 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9
Current overlap	16	Native recall	0.76
Jaccard	0.64	RMSD	-
HB strict	0	Strict recall	0.00
HB same residue+role	0	HB role recall	0.00
HB same residue	0	HB residue recall	0.00

Protein summary

200 residues

Protein target	T02	Atoms	3128
Residues	200	Chains	2
Residue summary	LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

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:NAP201

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
217	2.8221101969332563	-0.772931	-19.0049	1	20	16	0.76	0.00	-	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 -19.005kcal/mol

Ligand efficiency (LE) -0.5279kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.366

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

Heavy atom count 36HA

Physicochemical properties

Molecular weight 488.8Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.06

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 39.05kcal/mol

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

Docked FF energy 250.18kcal/mol

Minimised FF energy 211.13kcal/mol

SASA & burial

✓ computed

SASA (unbound) 790.4Å²

Total solvent-accessible surface area of free ligand

BSA total 726.9Å²

Buried surface area upon binding

BSA apolar 722.4Å²

Hydrophobic contacts buried

BSA polar 4.5Å²

Polar contacts buried

Fraction buried 92.0%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 99.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1863.7Å²

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 1677.9Å²

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

Complex non-polar SASA 600.1Å²

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