FAIRMol

OHD_TB2021_30

Pose ID 4801 Compound 2957 Pose 60

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
T08
T. brucei PTR1 T. brucei
Ligand OHD_TB2021_30
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
17.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.48, H-bond role recall 0.60
Burial
94%
Hydrophobic fit
88%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.374 kcal/mol/HA) ✓ Good fit quality (FQ -12.13) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Moderate strain (17.0 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (9)
Score
-31.605
kcal/mol
LE
-1.374
kcal/mol/HA
Fit Quality
-12.13
FQ (Leeson)
HAC
23
heavy atoms
MW
304
Da
LogP
0.68
cLogP
Strain ΔE
17.0 kcal/mol
SASA buried
94%
Lipo contact
88% BSA apolar/total
SASA unbound
550 Ų
Apolar buried
453 Ų

Interaction summary

HB 6 HY 23 PI 3 CLASH 1

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
Final rank0.047Score-31.605
Inter norm-1.412Intra norm0.038
Top1000noExcludedno
Contacts12H-bonds6
Artifact reasongeometry warning; 9 clashes; 2 protein contact clashes; 2 cofactor-context clashes
Residues
ARG14 ASP161 CYS168 GLY205 LEU263 MET163 NAP301 PHE97 PRO210 TRP221 TYR174 VAL206

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap10Native recall0.53
Jaccard0.48RMSD-
HB strict4Strict recall0.67
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
60 0.046746216921269436 -1.41246 -31.6051 6 12 10 0.53 0.60 - no Current
49 1.712367527102259 -1.07079 -21.2545 6 15 0 0.00 0.00 - no Open
60 2.2584766218910373 -0.844071 -21.1102 5 10 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 -31.605kcal/mol
Ligand efficiency (LE) -1.3741kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.128
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 304.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.68
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -50.25kcal/mol
Minimised FF energy -67.22kcal/mol

SASA & burial

✓ computed
SASA (unbound) 549.7Ų
Total solvent-accessible surface area of free ligand
BSA total 513.9Ų
Buried surface area upon binding
BSA apolar 452.5Ų
Hydrophobic contacts buried
BSA polar 61.4Ų
Polar contacts buried
Fraction buried 93.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1613.6Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 924.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)