FAIRMol

Z44349777

Pose ID 473 Compound 161 Pose 473

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T01
Human DHFR Human
Ligand Z44349777
PDB5SD8↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
31.7 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.57, Jaccard 0.48, H-bond role recall 0.80
Burial
80%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.923 kcal/mol/HA) ✓ Good fit quality (FQ -8.61) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Very high strain energy (31.7 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (10)
Score
-24.918
kcal/mol
LE
-0.923
kcal/mol/HA
Fit Quality
-8.61
FQ (Leeson)
HAC
27
heavy atoms
MW
387
Da
LogP
1.90
cLogP
Strain ΔE
31.7 kcal/mol
SASA buried
80%
Lipo contact
66% BSA apolar/total
SASA unbound
658 Ų
Apolar buried
349 Ų

Interaction summary

HB 7 HY 24 PI 2 CLASH 4
Final rank1.293Score-24.918
Inter norm-0.999Intra norm0.076
Top1000noExcludedno
Contacts16H-bonds7
Artifact reasongeometry warning; 10 clashes; 7 protein contact clashes; 1 severe cofactor-context clash; high strain Δ 31.7
Residues
ALA10 ARG29 ASN65 GLU31 GLY117 ILE8 LEU23 LEU28 NAP201 PHE32 PHE35 PRO27 TRP25 TYR122 VAL116 VAL9

Protein summary

200 residues
Protein targetT01Atoms3128
Residues200Chains2
Residue summaryLYS: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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5SD8Contacts21
PoseOpen native poseHB0
IFP residues
ALA10 ASN65 ASP22 GLN36 GLU31 GLY117 GLY21 ILE61 ILE8 LEU23 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9
Current overlap12Native recall0.57
Jaccard0.48RMSD-
HB strict3Strict recall0.60
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
473 1.2927990027273728 -0.999031 -24.9179 7 16 12 0.57 0.80 - no Current
361 4.743229079303923 -1.05115 -29.8407 13 17 0 0.00 0.00 - no Open
478 5.662619991575604 -0.839966 -25.3587 9 13 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -24.918kcal/mol
Ligand efficiency (LE) -0.9229kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.610
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 387.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.90
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -33.02kcal/mol
Minimised FF energy -64.67kcal/mol

SASA & burial

✓ computed
SASA (unbound) 658.4Ų
Total solvent-accessible surface area of free ligand
BSA total 528.4Ų
Buried surface area upon binding
BSA apolar 348.8Ų
Hydrophobic contacts buried
BSA polar 179.7Ų
Polar contacts buried
Fraction buried 80.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1541.8Ų
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 1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 607.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)