FAIRMol

Z56911531

Pose ID 1173 Compound 1028 Pose 495

DB fairmolDocking 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
T02
Human DHFR Human
Ligand Z56911531
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
51.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.57, Jaccard 0.46, H-bond role recall 0.20
Burial
94%
Hydrophobic fit
72%
Reason: strain 51.4 kcal/mol
strain ΔE 51.4 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.227 kcal/mol/HA) ✓ Good fit quality (FQ -10.83) ✓ Good H-bonds (4 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Extreme strain energy (51.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-28.218
kcal/mol
LE
-1.227
kcal/mol/HA
Fit Quality
-10.83
FQ (Leeson)
HAC
23
heavy atoms
MW
347
Da
LogP
2.81
cLogP
Final rank
3.8496
rank score
Inter norm
-1.321
normalised
Contacts
17
H-bonds 4
Strain ΔE
51.4 kcal/mol
SASA buried
94%
Lipo contact
72% BSA apolar/total
SASA unbound
545 Ų
Apolar buried
366 Ų

Interaction summary

HBD 2 HBA 2 HY 7 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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.
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
Jaccard0.46RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

200 residues
Protein targetT02Atoms3128
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
528 1.0580254495320864 -1.04038 -20.2108 7 12 0 0.00 0.00 - no Open
433 3.0456103007952593 -1.1748 -18.7928 11 19 0 0.00 0.00 - no Open
495 3.8496145283112764 -1.32078 -28.2185 4 17 12 0.57 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 -28.218kcal/mol
Ligand efficiency (LE) -1.2269kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.828
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 347.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.81
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 51.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 112.37kcal/mol
Minimised FF energy 61.01kcal/mol

SASA & burial

✓ computed
SASA (unbound) 545.1Ų
Total solvent-accessible surface area of free ligand
BSA total 509.7Ų
Buried surface area upon binding
BSA apolar 366.0Ų
Hydrophobic contacts buried
BSA polar 143.7Ų
Polar contacts buried
Fraction buried 93.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1466.3Ų
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 608.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)